diff --git a/.gitignore b/.gitignore index 7277c87b..d29d3933 100644 --- a/.gitignore +++ b/.gitignore @@ -87,7 +87,6 @@ cover/ *.pot # Django stuff: -*.log local_settings.py db.sqlite3 db.sqlite3-journal diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/commands.sh b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/commands.sh new file mode 100755 index 00000000..2e31bc08 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/commands.sh @@ -0,0 +1,3 @@ +gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +gmx mdrun -s water.tpr -o water.trr diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/confout.gro new file mode 100644 index 00000000..32347455 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.426 0.088 1.636-13.9673 12.4078 22.1878 + 1SOL HW1 2 0.352 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index 00000000..08ca1aa3 Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/ener.edr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/md.log b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/md.log new file mode 100644 index 00000000..43a612d0 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/md.log @@ -0,0 +1,484 @@ +Log file opened on Wed Jan 3 15:16:49 2024 +Host: FAIRmat-AreaC2-Rudzinski pid: 406916 rank ID: 0 number of ranks: 1 + :-) GROMACS - gmx mdrun, 2018.6 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra + Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru + Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus + Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl + Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola + Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov + Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2017, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2018.6 +Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_integrators_1frame/bd +Command line: + gmx mdrun -s water.tpr -o water.trr + +GROMACS version: 2018.6 +Precision: single +Memory model: 64 bit +MPI library: thread_mpi +OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) +GPU support: OpenCL +SIMD instructions: SSE2 +FFT library: fftw-3.3.8-sse2-avx +RDTSCP usage: disabled +TNG support: enabled +Hwloc support: hwloc-1.11.9 +Tracing support: disabled +Built on: 2019-05-12 20:18:02 +Built by: root@default-0e84dd72-7298-44a4-a670-e10728e370dd [CMAKE] +Build OS/arch: Linux 4.4.0-96-generic x86_64 +Build CPU vendor: Unknown +Build CPU brand: Unknown +Build CPU family: 0 Model: 0 Stepping: 0 +Build CPU features: Unknown +C compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc GNU 7.3.0 +C compiler flags: -msse2 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +C++ compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ GNU 7.3.0 +C++ compiler flags: -msse2 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +OpenCL include dir: /home/jfrudzinski/miniconda3/envs/martignac_2/include +OpenCL library: /home/jfrudzinski/miniconda3/envs/martignac_2/lib/libOpenCL.so +OpenCL version: 2.0 + +NOTE: Detection of GPUs failed. The API reported: + GROMACS cannot run tasks on a GPU. + +Running on 1 node with total 4 cores, 8 logical cores, 0 compatible GPUs +Hardware detected: + CPU info: + Vendor: Intel + Brand: 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz + Family: 6 Model: 140 Stepping: 1 + Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic + Number of AVX-512 FMA units: Cannot run AVX-512 detection - assuming 2 + Hardware topology: Full, with devices + Sockets, cores, and logical processors: + Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] + Numa nodes: + Node 0 (16138244096 bytes mem): 0 1 2 3 4 5 6 7 + Latency: + 0 + 0 1.00 + Caches: + L1: 49152 bytes, linesize 64 bytes, assoc. 12, shared 2 ways + L2: 1310720 bytes, linesize 64 bytes, assoc. 20, shared 2 ways + L3: 12582912 bytes, linesize 64 bytes, assoc. 12, shared 8 ways + PCI devices: + 0000:00:02.0 Id: 8086:9a49 Class: 0x0300 Numa: 0 + 0000:00:0e.0 Id: 8086:9a0b Class: 0x0104 Numa: 0 + 0000:00:14.3 Id: 8086:a0f0 Class: 0x0280 Numa: 0 + 0000:00:1f.6 Id: 8086:15fb Class: 0x0200 Numa: 0 + +Highest SIMD level requested by all nodes in run: AVX_512 +SIMD instructions selected at compile time: SSE2 +This program was compiled for different hardware than you are running on, +which could influence performance. + +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. +Lindahl +GROMACS: High performance molecular simulations through multi-level +parallelism from laptops to supercomputers +SoftwareX 1 (2015) pp. 19-25 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl +Tackling Exascale Software Challenges in Molecular Dynamics Simulations with +GROMACS +In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. +Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl +GROMACS 4.5: a high-throughput and highly parallel open source molecular +simulation toolkit +Bioinformatics 29 (2013) pp. 845-54 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl +GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable +molecular simulation +J. Chem. Theory Comput. 4 (2008) pp. 435-447 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. +Berendsen +GROMACS: Fast, Flexible and Free +J. Comp. Chem. 26 (2005) pp. 1701-1719 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +E. Lindahl and B. Hess and D. van der Spoel +GROMACS 3.0: A package for molecular simulation and trajectory analysis +J. Mol. Mod. 7 (2001) pp. 306-317 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +H. J. C. Berendsen, D. van der Spoel and R. van Drunen +GROMACS: A message-passing parallel molecular dynamics implementation +Comp. Phys. Comm. 91 (1995) pp. 43-56 +-------- -------- --- Thank You --- -------- -------- + +Input Parameters: + integrator = bd + tinit = 0 + dt = 0.0001 + nsteps = 1 + init-step = 0 + simulation-part = 1 + comm-mode = Linear + nstcomm = 1 + bd-fric = 0 + ld-seed = -536582013 + emtol = 10 + emstep = 0.01 + niter = 20 + fcstep = 0 + nstcgsteep = 1000 + nbfgscorr = 10 + rtpi = 0.05 + nstxout = 1 + nstvout = 1 + nstfout = 1 + nstlog = 1 + nstcalcenergy = 1 + nstenergy = 1 + nstxout-compressed = 0 + compressed-x-precision = 1000 + cutoff-scheme = Verlet + nstlist = 1 + ns-type = Grid + pbc = xyz + periodic-molecules = false + verlet-buffer-tolerance = 0.005 + rlist = 0.9 + coulombtype = PME + coulomb-modifier = Potential-shift + rcoulomb-switch = 0 + rcoulomb = 0.9 + epsilon-r = 1 + epsilon-rf = inf + vdw-type = Cut-off + vdw-modifier = Potential-shift + rvdw-switch = 0 + rvdw = 0.9 + DispCorr = EnerPres + table-extension = 1 + fourierspacing = 0.08 + fourier-nx = 24 + fourier-ny = 24 + fourier-nz = 24 + pme-order = 6 + ewald-rtol = 1e-06 + ewald-rtol-lj = 0.001 + lj-pme-comb-rule = Geometric + ewald-geometry = 0 + epsilon-surface = 0 + implicit-solvent = No + gb-algorithm = Still + nstgbradii = 1 + rgbradii = 1 + gb-epsilon-solvent = 80 + gb-saltconc = 0 + gb-obc-alpha = 1 + gb-obc-beta = 0.8 + gb-obc-gamma = 4.85 + gb-dielectric-offset = 0.009 + sa-algorithm = Ace-approximation + sa-surface-tension = 2.05016 + tcoupl = No + nsttcouple = -1 + nh-chain-length = 0 + print-nose-hoover-chain-variables = false + pcoupl = No + pcoupltype = Isotropic + nstpcouple = -1 + tau-p = 1 + compressibility (3x3): + compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p (3x3): + ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + refcoord-scaling = No + posres-com (3): + posres-com[0]= 0.00000e+00 + posres-com[1]= 0.00000e+00 + posres-com[2]= 0.00000e+00 + posres-comB (3): + posres-comB[0]= 0.00000e+00 + posres-comB[1]= 0.00000e+00 + posres-comB[2]= 0.00000e+00 + QMMM = false + QMconstraints = 0 + QMMMscheme = 0 + MMChargeScaleFactor = 1 +qm-opts: + ngQM = 0 + constraint-algorithm = Lincs + continuation = false + Shake-SOR = false + shake-tol = 0.0001 + lincs-order = 4 + lincs-iter = 1 + lincs-warnangle = 30 + nwall = 0 + wall-type = 9-3 + wall-r-linpot = -1 + wall-atomtype[0] = -1 + wall-atomtype[1] = -1 + wall-density[0] = 0 + wall-density[1] = 0 + wall-ewald-zfac = 3 + pull = false + awh = false + rotation = false + interactiveMD = false + disre = No + disre-weighting = Conservative + disre-mixed = false + dr-fc = 1000 + dr-tau = 0 + nstdisreout = 100 + orire-fc = 0 + orire-tau = 0 + nstorireout = 100 + free-energy = no + cos-acceleration = 0 + deform (3x3): + deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + simulated-tempering = false + swapcoords = no + userint1 = 0 + userint2 = 0 + userint3 = 0 + userint4 = 0 + userreal1 = 0 + userreal2 = 0 + userreal3 = 0 + userreal4 = 0 + applied-forces: + electric-field: + x: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + y: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + z: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 +grpopts: + nrdf: 1293 + ref-t: 298 + tau-t: 0.5 +annealing: No +annealing-npoints: 0 + acc: 0 0 0 + nfreeze: N N N + energygrp-flags[ 0]: 0 + + +Using 1 MPI thread +Using 8 OpenMP threads + +Pinning threads with an auto-selected logical core stride of 1 +System total charge: 0.000 +Will do PME sum in reciprocal space for electrostatic interactions. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen +A smooth particle mesh Ewald method +J. Chem. Phys. 103 (1995) pp. 8577-8592 +-------- -------- --- Thank You --- -------- -------- + +Using a Gaussian width (1/beta) of 0.260197 nm for Ewald +Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-06 +Initialized non-bonded Ewald correction tables, spacing: 8.41e-04 size: 1071 + +Long Range LJ corr.: 2.9078e-04 +Generated table with 950 data points for Ewald. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ6. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ12. +Tabscale = 500 points/nm + +Using SIMD 4x4 nonbonded short-range kernels + +Using a 4x4 pair-list setup: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm +At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm + +Using geometric Lennard-Jones combination rule + +Removing pbc first time + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Miyamoto and P. A. Kollman +SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid +Water Models +J. Comp. Chem. 13 (1992) pp. 952-962 +-------- -------- --- Thank You --- -------- -------- + + +Intra-simulation communication will occur every 1 steps. +Center of mass motion removal mode is Linear +We have the following groups for center of mass motion removal: + 0: rest +There are: 648 Atoms + +Constraining the starting coordinates (step 0) +RMS relative constraint deviation after constraining: 0.00e+00 + +Started mdrun on rank 0 Wed Jan 3 15:16:50 2024 + Step Time + 0 0.00000 + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.98181e+03 -1.08747e+02 -1.21912e+04 1.28385e+02 -1.01898e+04 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 9.27995e+02 -9.26177e+03 1.72641e+02 -2.80811e+02 1.28268e+04 + + Step Time + 1 0.00010 + +Writing checkpoint, step 1 at Wed Jan 3 15:16:50 2024 + + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.96138e+03 -1.08747e+02 -1.17446e+04 1.72185e+02 -9.71979e+03 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.94505e+03 -7.77474e+03 3.61850e+02 -2.80811e+02 1.54564e+04 + + <====== ############### ==> + <==== A V E R A G E S ====> + <== ############### ======> + + Statistics over 2 steps using 2 frames + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97160e+03 -1.08747e+02 -1.19679e+04 1.50285e+02 -9.95478e+03 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.43652e+03 -8.51825e+03 2.67245e+02 -2.80811e+02 1.41416e+04 + + Total Virial (kJ/mol) + -2.25567e+03 -3.09550e+01 1.24819e+02 + -3.09511e+01 -2.32523e+03 -1.17361e+02 + 1.24815e+02 -1.17364e+02 -2.21069e+03 + + Pressure (bar) + 1.41676e+04 1.72172e+02 -6.10476e+02 + 1.72152e+02 1.43984e+04 5.19562e+02 + -6.10456e+02 5.19580e+02 1.38588e+04 + + + M E G A - F L O P S A C C O U N T I N G + + NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels + RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table + W3=SPC/TIP3p W4=TIP4p (single or pairs) + V&F=Potential and force V=Potential only F=Force only + + Computing: M-Number M-Flops % Flops +----------------------------------------------------------------------------- + Pair Search distance check 0.306912 2.762 8.6 + NxN QSTab Elec. + LJ [V&F] 0.206104 12.160 37.9 + NxN QSTab Elec. [V&F] 0.201528 8.263 25.8 + Calc Weights 0.003888 0.140 0.4 + Spread Q Bspline 0.279936 0.560 1.7 + Gather F Bspline 0.279936 1.680 5.2 + 3D-FFT 0.760588 6.085 19.0 + Solve PME 0.001152 0.074 0.2 + Shift-X 0.001296 0.008 0.0 + Virial 0.001386 0.025 0.1 + Stop-CM 0.001944 0.019 0.1 + Calc-Ekin 0.001944 0.052 0.2 + Constraint-V 0.001296 0.010 0.0 + Constraint-Vir 0.001296 0.031 0.1 + Settle 0.000648 0.209 0.7 +----------------------------------------------------------------------------- + Total 32.078 100.0 +----------------------------------------------------------------------------- + + + R E A L C Y C L E A N D T I M E A C C O U N T I N G + +On 1 MPI rank, each using 8 OpenMP threads + + Computing: Num Num Call Wall time Giga-Cycles + Ranks Threads Count (s) total sum % +----------------------------------------------------------------------------- + Neighbor search 1 8 2 0.002 0.027 8.7 + Force 1 8 2 0.000 0.004 1.4 + PME mesh 1 8 2 0.000 0.005 1.5 + NB X/F buffer ops. 1 8 2 0.000 0.000 0.0 + Write traj. 1 8 2 0.011 0.166 53.7 + Update 1 8 2 0.007 0.100 32.3 + Constraints 1 8 2 0.000 0.000 0.1 + Rest 0.000 0.007 2.3 +----------------------------------------------------------------------------- + Total 0.021 0.309 100.0 +----------------------------------------------------------------------------- + Breakdown of PME mesh computation +----------------------------------------------------------------------------- + PME spread 1 8 2 0.000 0.002 0.6 + PME gather 1 8 2 0.000 0.001 0.5 + PME 3D-FFT 1 8 4 0.000 0.001 0.3 + PME solve Elec 1 8 2 0.000 0.000 0.1 +----------------------------------------------------------------------------- + + Core t (s) Wall t (s) (%) + Time: 0.171 0.021 800.0 + (ns/day) (hour/ns) +Performance: 0.808 29.685 +Finished mdrun on rank 0 Wed Jan 3 15:16:50 2024 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/mdout.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/mdout.mdp new file mode 100644 index 00000000..d9b2ef35 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/mdout.mdp @@ -0,0 +1,353 @@ +; +; File 'mdout.mdp' was generated +; By user: jfrudzinski (1000) +; On host: FAIRmat-AreaC2-Rudzinski +; At date: Wed Jan 3 15:16:49 2024 +; +; Created by: +; :-) GROMACS - gmx grompp, 2018.6 (-: +; +; Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +; Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +; Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_integrators_1frame/bd +; Command line: +; gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +; VARIOUS PREPROCESSING OPTIONS +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/roe +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ +; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) +define = + +; RUN CONTROL PARAMETERS +integrator = bd +; Start time and timestep in ps +tinit = 0.0 +dt = 0.0001 +nsteps = 1 +; For exact run continuation or redoing part of a run +init-step = 0 +; Part index is updated automatically on checkpointing (keeps files separate) +simulation-part = 1 +; mode for center of mass motion removal +comm-mode = linear +; number of steps for center of mass motion removal +nstcomm = 1 +; group(s) for center of mass motion removal +comm-grps = + +; LANGEVIN DYNAMICS OPTIONS +; Friction coefficient (amu/ps) and random seed +bd-fric = 0 +ld-seed = -1 + +; ENERGY MINIMIZATION OPTIONS +; Force tolerance and initial step-size +emtol = 10 +emstep = 0.01 +; Max number of iterations in relax-shells +niter = 20 +; Step size (ps^2) for minimization of flexible constraints +fcstep = 0 +; Frequency of steepest descents steps when doing CG +nstcgsteep = 1000 +nbfgscorr = 10 + +; TEST PARTICLE INSERTION OPTIONS +rtpi = 0.05 + +; OUTPUT CONTROL OPTIONS +; Output frequency for coords (x), velocities (v) and forces (f) +nstxout = 1 +nstvout = 1 +nstfout = 1 +; Output frequency for energies to log file and energy file +nstlog = 1 +nstcalcenergy = 100 +nstenergy = 1 +; Output frequency and precision for .xtc file +nstxout-compressed = 0 +compressed-x-precision = 1000 +; This selects the subset of atoms for the compressed +; trajectory file. You can select multiple groups. By +; default, all atoms will be written. +compressed-x-grps = +; Selection of energy groups +energygrps = System + +; NEIGHBORSEARCHING PARAMETERS +; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) +cutoff-scheme = Verlet +; nblist update frequency +nstlist = 1 +; ns algorithm (simple or grid) +ns_type = grid +; Periodic boundary conditions: xyz, no, xy +pbc = xyz +periodic-molecules = no +; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, +; a value of -1 means: use rlist +verlet-buffer-tolerance = 0.005 +; nblist cut-off +rlist = 0.9 +; long-range cut-off for switched potentials + +; OPTIONS FOR ELECTROSTATICS AND VDW +; Method for doing electrostatics +coulombtype = PME +coulomb-modifier = Potential-shift-Verlet +rcoulomb-switch = 0 +rcoulomb = 0.9 +; Relative dielectric constant for the medium and the reaction field +epsilon-r = 1 +epsilon-rf = 0 +; Method for doing Van der Waals +vdwtype = cutoff +vdw-modifier = Potential-shift-Verlet +; cut-off lengths +rvdw-switch = 0 +rvdw = 0.9 +; Apply long range dispersion corrections for Energy and Pressure +DispCorr = EnerPres +; Extension of the potential lookup tables beyond the cut-off +table-extension = 1 +; Separate tables between energy group pairs +energygrp-table = +; Spacing for the PME/PPPM FFT grid +fourierspacing = 0.08 +; FFT grid size, when a value is 0 fourierspacing will be used +fourier-nx = 0 +fourier-ny = 0 +fourier-nz = 0 +; EWALD/PME/PPPM parameters +pme_order = 6 +ewald_rtol = 1e-06 +ewald-rtol-lj = 0.001 +lj-pme-comb-rule = Geometric +ewald-geometry = 3d +epsilon-surface = 0 + +; IMPLICIT SOLVENT ALGORITHM +implicit-solvent = No + +; GENERALIZED BORN ELECTROSTATICS +; Algorithm for calculating Born radii +gb-algorithm = Still +; Frequency of calculating the Born radii inside rlist +nstgbradii = 1 +; Cutoff for Born radii calculation; the contribution from atoms +; between rlist and rgbradii is updated every nstlist steps +rgbradii = 1 +; Dielectric coefficient of the implicit solvent +gb-epsilon-solvent = 80 +; Salt concentration in M for Generalized Born models +gb-saltconc = 0 +; Scaling factors used in the OBC GB model. Default values are OBC(II) +gb-obc-alpha = 1 +gb-obc-beta = 0.8 +gb-obc-gamma = 4.85 +gb-dielectric-offset = 0.009 +sa-algorithm = Ace-approximation +; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA +; The value -1 will set default value for Still/HCT/OBC GB-models. +sa-surface-tension = -1 + +; OPTIONS FOR WEAK COUPLING ALGORITHMS +; Temperature coupling +tcoupl = No +nsttcouple = -1 +nh-chain-length = 10 +print-nose-hoover-chain-variables = no +; Groups to couple separately +tc_grps = System +; Time constant (ps) and reference temperature (K) +tau_t = 0.5 +ref_t = 298 +; pressure coupling +pcoupl = No +pcoupltype = Isotropic +nstpcouple = -1 +; Time constant (ps), compressibility (1/bar) and reference P (bar) +tau-p = 1 +compressibility = +ref-p = +; Scaling of reference coordinates, No, All or COM +refcoord-scaling = No + +; OPTIONS FOR QMMM calculations +QMMM = no +; Groups treated Quantum Mechanically +QMMM-grps = +; QM method +QMmethod = +; QMMM scheme +QMMMscheme = normal +; QM basisset +QMbasis = +; QM charge +QMcharge = +; QM multiplicity +QMmult = +; Surface Hopping +SH = +; CAS space options +CASorbitals = +CASelectrons = +SAon = +SAoff = +SAsteps = +; Scale factor for MM charges +MMChargeScaleFactor = 1 + +; SIMULATED ANNEALING +; Type of annealing for each temperature group (no/single/periodic) +annealing = +; Number of time points to use for specifying annealing in each group +annealing-npoints = +; List of times at the annealing points for each group +annealing-time = +; Temp. at each annealing point, for each group. +annealing-temp = + +; GENERATE VELOCITIES FOR STARTUP RUN +gen_vel = yes +gen_temp = 298 +gen_seed = 173529 + +; OPTIONS FOR BONDS +constraints = none +; Type of constraint algorithm +constraint-algorithm = Lincs +; Do not constrain the start configuration +continuation = no +; Use successive overrelaxation to reduce the number of shake iterations +Shake-SOR = no +; Relative tolerance of shake +shake-tol = 0.0001 +; Highest order in the expansion of the constraint coupling matrix +lincs-order = 4 +; Number of iterations in the final step of LINCS. 1 is fine for +; normal simulations, but use 2 to conserve energy in NVE runs. +; For energy minimization with constraints it should be 4 to 8. +lincs-iter = 1 +; Lincs will write a warning to the stderr if in one step a bond +; rotates over more degrees than +lincs-warnangle = 30 +; Convert harmonic bonds to morse potentials +morse = no + +; ENERGY GROUP EXCLUSIONS +; Pairs of energy groups for which all non-bonded interactions are excluded +energygrp-excl = + +; WALLS +; Number of walls, type, atom types, densities and box-z scale factor for Ewald +nwall = 0 +wall-type = 9-3 +wall-r-linpot = -1 +wall-atomtype = +wall-density = +wall-ewald-zfac = 3 + +; COM PULLING +pull = no + +; AWH biasing +awh = no + +; ENFORCED ROTATION +; Enforced rotation: No or Yes +rotation = no + +; Group to display and/or manipulate in interactive MD session +IMD-group = + +; NMR refinement stuff +; Distance restraints type: No, Simple or Ensemble +disre = No +; Force weighting of pairs in one distance restraint: Conservative or Equal +disre-weighting = Conservative +; Use sqrt of the time averaged times the instantaneous violation +disre-mixed = no +disre-fc = 1000 +disre-tau = 0 +; Output frequency for pair distances to energy file +nstdisreout = 100 +; Orientation restraints: No or Yes +orire = no +; Orientation restraints force constant and tau for time averaging +orire-fc = 0 +orire-tau = 0 +orire-fitgrp = +; Output frequency for trace(SD) and S to energy file +nstorireout = 100 + +; Free energy variables +free-energy = no +couple-moltype = +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q +couple-intramol = no +init-lambda = -1 +init-lambda-state = -1 +delta-lambda = 0 +nstdhdl = 50 +fep-lambdas = +mass-lambdas = +coul-lambdas = +vdw-lambdas = +bonded-lambdas = +restraint-lambdas = +temperature-lambdas = +calc-lambda-neighbors = 1 +init-lambda-weights = +dhdl-print-energy = no +sc-alpha = 0 +sc-power = 1 +sc-r-power = 6 +sc-sigma = 0.3 +sc-coul = no +separate-dhdl-file = yes +dhdl-derivatives = yes +dh_hist_size = 0 +dh_hist_spacing = 0.1 + +; Non-equilibrium MD stuff +acc-grps = +accelerate = +freezegrps = +freezedim = +cos-acceleration = 0 +deform = + +; simulated tempering variables +simulated-tempering = no +simulated-tempering-scaling = geometric +sim-temp-low = 300 +sim-temp-high = 300 + +; Ion/water position swapping for computational electrophysiology setups +; Swap positions along direction: no, X, Y, Z +swapcoords = no +adress = no + +; User defined thingies +user1-grps = +user2-grps = +userint1 = 0 +userint2 = 0 +userint3 = 0 +userint4 = 0 +userreal1 = 0 +userreal2 = 0 +userreal3 = 0 +userreal4 = 0 +; Electric fields +; Format for electric-field-x, etc. is: four real variables: +; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), +; and sigma (ps) width of the pulse. Omega = 0 means static field, +; sigma = 0 means no pulse, leaving the field to be a cosine function. +electric-field-x = 0 0 0 0 +electric-field-y = 0 0 0 0 +electric-field-z = 0 0 0 0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/state.cpt b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/state.cpt new file mode 100644 index 00000000..a96c3a6a Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/state.cpt differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.298.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.298.mdp new file mode 100644 index 00000000..f602ee37 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.298.mdp @@ -0,0 +1,52 @@ +; Preprocessing +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ + +; Run Control +integrator = bd +tinit = 0.0 +dt = 0.0001 ; 1.0 fs +nsteps = 1 ; 20 ns +nstcomm = 1 ; no. steps between removing com motion +comm-mode = linear ; remove com translation + +; Output Control +nstxout = 1 ; no. steps between printing coords to trr file => 1ps +nstvout = 1 ; no. steps between printing veloc to trr file +nstfout = 1 ; no. steps between printing forces to trr file => 1ps +nstlog = 1 ; no. steps between printing energy to log file => 1ps +nstenergy = 1 ; no. steps between printing energy to edr file => 1ps +nstxtcout = 0 ; no. stpes between printing coords to xtc file +energygrps = System ; groups for writing energy file + +; Neighbor searching +nstlist = 1 ; update neighbor list every step +ns_type = grid ; check neighbor list using grid +rlist = 0.9 ; cutoff distance (nm) for short-range neighbor list + +; Electrostatics and VdW +coulombtype = PME ; fast particle-mesh ewald electrostatics +rcoulomb = 0.9 ; distance for the Coulomb cut-off +vdwtype = cutoff ; truncated LJ interactions +rvdw = 0.9 ; distance for LJ cut-off +DispCorr = EnerPres ; apply long range disp. correct. for Energy/Pres +fourierspacing = 0.08 ; max grid spacing fr FFT grid in PME +pme_order = 6 ; interpolation order for PME +ewald_rtol = 1e-06 ; relative strength of direct potential at cutoff +optimize_fft = yes ; optimize fft_grids + +; Temperature Coupling +;tcoupl = nose-hoover ; nose-hoover for correct ensemble +tc_grps = System ; groups to couple separtly to temp. bath +tau_t = 0.5 ; time constant for coupling +ref_t = 298 ; ref. temperature for coupling + +; Velocity generation +gen_vel = yes ; generate velocities with Max. dist. +gen_temp = 298 ; temp. for Max. dist. +gen_seed = 173529 ; for random number generator + +; Pressure coupling +;pcoupl = Parrinello-Rahman +;tau-p = 5.0 +;compressibility = 7.4e-5 +;ref-p = 1.0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.confout.gro new file mode 100644 index 00000000..0244d504 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.confout.gro 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0.873 1.381 1.548 -0.6467 -1.3305 -0.3211 + 178SOL OW 532 0.703 0.578 0.619 0.2456 -0.5121 -0.0258 + 178SOL HW1 533 0.706 0.644 0.544 0.1046 0.1791 0.5645 + 178SOL HW2 534 0.609 0.546 0.632 0.2652 -0.6092 -0.1228 + 179SOL OW 535 1.069 1.528 1.490 -0.4791 0.3219 0.1074 + 179SOL HW1 536 1.089 1.431 1.506 1.6026 0.3421 -2.1362 + 179SOL HW2 537 1.153 1.581 1.492 -1.3336 1.7645 -0.8926 + 180SOL OW 538 0.331 1.507 0.882 0.0830 0.6824 0.3473 + 180SOL HW1 539 0.351 1.445 0.958 0.4365 0.0094 -0.2907 + 180SOL HW2 540 0.235 1.499 0.857 0.6896 -1.4571 -1.3748 + 181SOL OW 541 1.370 0.007 0.942 0.3182 -0.3568 -0.3435 + 181SOL HW1 542 1.432 -0.071 0.940 0.0645 -0.5854 0.5377 + 181SOL HW2 543 1.282 -0.018 0.902 -0.8327 -1.4792 2.7400 + 182SOL OW 544 0.253 0.428 0.457 -0.0183 0.3143 0.3329 + 182SOL HW1 545 0.311 0.351 0.430 -0.1553 1.1020 -2.4236 + 182SOL HW2 546 0.170 0.393 0.502 1.6909 -0.9043 2.6201 + 183SOL OW 547 0.286 0.097 1.177 0.5078 -0.0262 -0.1346 + 183SOL HW1 548 0.219 0.171 1.184 -0.0027 -0.3660 -1.2136 + 183SOL HW2 549 0.367 0.130 1.128 1.1385 0.3882 1.1809 + 184SOL OW 550 0.025 1.844 1.398 0.8241 0.0883 -0.4432 + 184SOL HW1 551 0.099 1.895 1.442 1.8365 -1.9952 0.2967 + 184SOL HW2 552 -0.012 1.776 1.461 -0.4736 -0.1561 -1.4373 + 185SOL OW 553 0.534 0.658 1.575 -0.3340 0.3639 -0.0368 + 185SOL HW1 554 0.574 0.664 1.667 0.3355 -1.0454 -0.2294 + 185SOL HW2 555 0.607 0.657 1.507 -0.6335 -2.9360 -0.3589 + 186SOL OW 556 1.418 0.775 0.820 -0.0169 1.0421 -0.8445 + 186SOL HW1 557 1.378 0.691 0.857 0.7531 1.3106 0.6462 + 186SOL HW2 558 1.398 0.782 0.723 -0.6095 -0.5640 -0.8452 + 187SOL OW 559 0.222 0.944 1.345 -0.2158 0.3297 -0.7016 + 187SOL HW1 560 0.131 0.904 1.335 -0.6758 0.9556 0.9203 + 187SOL HW2 561 0.226 0.999 1.428 1.2918 1.2851 -1.3770 + 188SOL OW 562 0.914 0.467 0.189 0.6525 0.6939 0.0840 + 188SOL HW1 563 0.871 0.549 0.227 -0.0617 0.1423 0.4674 + 188SOL HW2 564 0.873 0.447 0.100 0.4158 0.4051 0.2610 + 189SOL OW 565 0.801 1.764 1.597 0.0175 0.4390 0.1863 + 189SOL HW1 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0.5478 -0.5495 + 195SOL HW1 584 0.747 1.197 0.604 -0.5919 0.8796 -2.7776 + 195SOL HW2 585 0.604 1.180 0.680 0.7884 -0.3959 -0.4194 + 196SOL OW 586 1.379 0.250 1.783 0.0082 -0.7042 0.3366 + 196SOL HW1 587 1.419 0.159 1.771 2.8172 0.8867 -3.3603 + 196SOL HW2 588 1.436 0.303 1.846 -0.5107 -0.8573 0.9364 + 197SOL OW 589 1.406 0.936 0.182 0.4528 -0.1813 0.0754 + 197SOL HW1 590 1.402 0.861 0.116 0.2006 -1.4207 1.4793 + 197SOL HW2 591 1.314 0.957 0.216 0.8623 -1.2400 1.8888 + 198SOL OW 592 0.030 0.412 1.436 0.2007 -0.0565 -0.4994 + 198SOL HW1 593 0.098 0.476 1.400 -0.3590 1.3329 0.8709 + 198SOL HW2 594 -0.018 0.453 1.513 -1.5666 -1.3714 -0.8498 + 199SOL OW 595 0.013 1.493 0.579 -0.5266 -0.7272 0.0410 + 199SOL HW1 596 0.039 1.479 0.675 -1.1788 1.6396 0.5768 + 199SOL HW2 597 -0.078 1.455 0.563 -1.3122 0.7763 0.8986 + 200SOL OW 598 0.446 0.239 1.024 0.0321 -0.2285 0.0174 + 200SOL HW1 599 0.426 0.256 0.928 -0.6769 0.6990 0.3210 + 200SOL HW2 600 0.440 0.325 1.075 1.7030 -0.4725 0.6645 + 201SOL OW 601 0.389 0.194 0.371 0.3108 -0.2167 0.5535 + 201SOL HW1 602 0.390 0.206 0.272 -0.3545 0.4874 0.6282 + 201SOL HW2 603 0.331 0.115 0.394 0.0047 -0.0376 0.4087 + 202SOL OW 604 0.672 1.424 0.815 -0.5655 0.8860 -0.1168 + 202SOL HW1 605 0.659 1.346 0.753 1.9136 -0.9085 1.5104 + 202SOL HW2 606 0.730 1.492 0.770 -0.6763 0.6517 -0.6213 + 203SOL OW 607 0.088 0.919 0.941 0.4703 0.3888 0.1022 + 203SOL HW1 608 0.118 0.832 0.980 -0.9147 -0.1690 -0.0698 + 203SOL HW2 609 -0.006 0.938 0.969 1.1561 2.4272 1.1431 + 204SOL OW 610 1.613 1.447 0.506 -0.2397 0.1224 -0.4911 + 204SOL HW1 611 1.574 1.455 0.414 -0.6147 -2.1473 -0.5397 + 204SOL HW2 612 1.539 1.443 0.573 0.0323 3.0606 0.0867 + 205SOL OW 613 1.801 1.172 1.523 -0.1389 0.0380 0.7452 + 205SOL HW1 614 1.813 1.262 1.566 -0.0595 0.0259 0.7478 + 205SOL HW2 615 1.830 1.176 1.427 -1.0958 0.2748 0.4670 + 206SOL OW 616 1.671 1.161 0.622 0.0381 -0.1968 -0.8982 + 206SOL HW1 617 1.659 1.062 0.624 1.0081 -0.2945 0.2200 + 206SOL HW2 618 1.665 1.194 0.528 -3.4793 -0.9138 -0.9865 + 207SOL OW 619 0.744 0.684 1.371 -0.4972 -0.4176 0.1462 + 207SOL HW1 620 0.819 0.647 1.316 -0.8700 -0.5741 -0.2655 + 207SOL HW2 621 0.664 0.697 1.313 -0.0811 1.9892 0.0593 + 208SOL OW 622 0.821 0.317 1.194 0.4536 0.4539 -0.3308 + 208SOL HW1 623 0.766 0.361 1.123 1.4276 0.6847 -0.9606 + 208SOL HW2 624 0.768 0.311 1.279 -0.1401 1.6828 -0.6050 + 209SOL OW 625 1.664 1.037 1.689 -0.3971 0.4743 0.3950 + 209SOL HW1 626 1.571 1.024 1.655 -0.4077 -0.2767 0.7076 + 209SOL HW2 627 1.711 1.105 1.632 -0.9022 0.3384 -0.1894 + 210SOL OW 628 1.819 0.231 0.807 -0.1924 0.5243 -0.1692 + 210SOL HW1 629 1.852 0.144 0.844 1.0633 0.7808 -0.6607 + 210SOL HW2 630 1.720 0.239 0.823 0.0839 0.0674 2.0047 + 211SOL OW 631 0.979 1.242 0.144 -0.2018 0.2018 -0.0354 + 211SOL HW1 632 0.938 1.316 0.090 -0.6232 -0.6929 -0.9633 + 211SOL HW2 633 0.946 1.247 0.238 -0.1197 1.2714 -0.0561 + 212SOL OW 634 0.778 0.948 0.748 0.5845 0.0149 -0.7815 + 212SOL HW1 635 0.818 1.006 0.676 -0.1841 1.1423 -0.3163 + 212SOL HW2 636 0.695 0.991 0.783 1.4375 -0.0808 1.4255 + 213SOL OW 637 1.814 1.673 1.613 -0.0991 0.5855 0.0909 + 213SOL HW1 638 1.826 1.683 1.712 0.1001 -0.7483 0.2122 + 213SOL HW2 639 1.873 1.599 1.580 -0.2204 0.9765 -1.0148 + 214SOL OW 640 0.068 1.175 1.260 0.2612 0.5460 0.5693 + 214SOL HW1 641 0.147 1.235 1.273 0.1725 0.8319 -0.1693 + 214SOL HW2 642 0.100 1.081 1.245 0.4518 0.6382 0.3995 + 215SOL OW 643 1.089 0.245 0.891 -0.1119 0.5785 0.4751 + 215SOL HW1 644 0.994 0.267 0.866 -0.3021 -0.0338 0.6459 + 215SOL HW2 645 1.099 0.146 0.898 0.6144 0.6299 0.1871 + 216SOL OW 646 1.135 1.550 0.658 0.1441 0.6409 -0.1721 + 216SOL HW1 647 1.078 1.522 0.736 0.3615 1.9482 0.4795 + 216SOL HW2 648 1.131 1.480 0.587 0.5499 -0.9515 1.3195 + 1.86060 1.86060 1.86060 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.top b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.top new file mode 100644 index 00000000..132cf50f --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.top @@ -0,0 +1,16 @@ +; +; +; Topology file for spce water +; +; +; +#include "oplsaa.ff/forcefield.itp" + +#include "oplsaa.ff/spce.itp" + +[ system ] +spce water + +[ molecules ] +SOL 216 + diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.tpr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.tpr new file mode 100644 index 00000000..761097f1 Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.tpr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.trr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.trr new file mode 100644 index 00000000..4dcc34be Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/water.trr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/commands.sh b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/commands.sh new file mode 100755 index 00000000..2e31bc08 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/commands.sh @@ -0,0 +1,3 @@ +gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +gmx mdrun -s water.tpr -o water.trr diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/confout.gro new file mode 100644 index 00000000..f32d03ab --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.427 0.088 1.634 0.0799 0.6255 -0.3199 + 1SOL HW1 2 0.351 0.152 1.636 -0.7159 -0.3158 0.2600 + 1SOL HW2 3 0.395 -0.000 1.599 1.0662 0.4174 -0.7319 + 2SOL OW 4 0.365 0.989 0.648 0.2276 -0.9319 -0.3083 + 2SOL HW1 5 0.376 0.912 0.585 -0.7199 -1.6616 0.3936 + 2SOL HW2 6 0.274 1.029 0.636 -0.0767 -1.2803 0.8165 + 3SOL OW 7 1.293 1.628 1.681 0.0957 0.2474 -0.5798 + 3SOL HW1 8 1.334 1.698 1.741 0.8086 -0.3746 -0.3393 + 3SOL HW2 9 1.364 1.565 1.650 -0.4451 0.0000 -1.3077 + 4SOL OW 10 0.922 1.027 1.587 -0.3811 -0.1014 0.3894 + 4SOL HW1 11 0.949 1.121 1.566 0.9947 -0.5019 0.3565 + 4SOL HW2 12 0.938 1.009 1.684 -0.3773 -0.3932 0.3356 + 5SOL OW 13 0.870 1.326 0.395 -0.6486 0.2653 0.0676 + 5SOL HW1 14 0.954 1.366 0.434 -0.8071 -1.2126 1.9796 + 5SOL HW2 15 0.792 1.382 0.421 -0.4612 0.7086 -0.3074 + 6SOL OW 16 0.300 0.862 0.125 -0.1237 -0.5483 0.6545 + 6SOL HW1 17 0.251 0.909 0.051 -1.0818 1.0534 2.2755 + 6SOL HW2 18 0.301 0.920 0.206 1.7744 -1.8827 1.6173 + 7SOL OW 19 1.513 1.574 0.936 0.3845 -0.4423 -0.5033 + 7SOL HW1 20 1.574 1.494 0.938 -0.2265 -0.8995 0.7859 + 7SOL HW2 21 1.442 1.562 1.006 -0.6017 0.5391 -1.3396 + 8SOL OW 22 1.705 1.514 1.173 -0.1703 -0.3617 -0.3613 + 8SOL HW1 23 1.787 1.568 1.154 0.2615 -1.0359 -0.4499 + 8SOL HW2 24 1.625 1.574 1.176 0.3731 0.3450 0.0718 + 9SOL OW 25 1.346 0.399 0.373 -0.2210 -0.0453 -0.6579 + 9SOL HW1 26 1.269 0.405 0.437 0.9618 0.9075 0.7221 + 9SOL HW2 27 1.330 0.324 0.309 -1.3331 -1.1950 0.9227 + 10SOL OW 28 1.416 0.982 1.612 -0.4653 -0.1623 -0.9723 + 10SOL HW1 29 1.364 0.896 1.616 0.1011 -0.4800 -0.4025 + 10SOL HW2 30 1.380 1.039 1.538 -2.3810 0.1175 0.1452 + 11SOL OW 31 0.580 1.437 1.073 -0.2636 -0.1720 -0.3128 + 11SOL HW1 32 0.642 1.501 1.117 0.1267 1.7454 -3.4491 + 11SOL HW2 33 0.587 1.447 0.974 -1.6015 -3.7883 -0.8669 + 12SOL OW 34 0.427 0.542 0.668 0.3572 0.7269 0.0564 + 12SOL HW1 35 0.376 0.513 0.587 -0.4496 2.2762 0.0104 + 12SOL HW2 36 0.375 0.611 0.719 0.8256 -0.2659 1.9441 + 13SOL OW 37 1.495 0.945 1.174 -1.1496 -0.4871 0.1961 + 13SOL HW1 38 1.551 0.866 1.152 -1.0453 -0.6155 0.9270 + 13SOL HW2 39 1.466 0.990 1.089 2.7603 1.4866 -0.2371 + 14SOL OW 40 1.416 1.196 0.728 -0.3799 -0.4798 0.0428 + 14SOL HW1 41 1.405 1.294 0.713 0.6089 -0.0874 1.8090 + 14SOL HW2 42 1.484 1.159 0.665 1.4638 0.5561 1.3979 + 15SOL OW 43 0.620 0.002 0.834 0.7183 -0.2985 -0.1200 + 15SOL HW1 44 0.575 -0.006 0.923 1.9424 0.6668 0.6035 + 15SOL HW2 45 0.570 0.067 0.777 1.3506 0.9883 0.7819 + 16SOL OW 46 1.846 0.346 0.269 -0.1833 -0.3912 0.0197 + 16SOL HW1 47 1.759 0.390 0.292 -0.9083 -1.0920 -1.3166 + 16SOL HW2 48 1.883 0.302 0.351 -1.7801 -1.2552 0.3076 + 17SOL OW 49 0.692 0.116 1.700 -0.6609 -0.4039 0.1051 + 17SOL HW1 50 0.692 0.127 1.799 -0.2195 3.9237 -0.2897 + 17SOL HW2 51 0.598 0.117 1.666 -0.7342 -0.1547 0.3151 + 18SOL OW 52 0.456 1.027 1.253 0.0478 0.5022 -0.3709 + 18SOL HW1 53 0.482 1.102 1.313 -1.2531 0.8006 -0.1725 + 18SOL HW2 54 0.374 0.981 1.288 -1.0706 1.0375 -2.1774 + 19SOL OW 55 1.527 1.387 1.709 0.4995 0.8600 0.3688 + 19SOL HW1 56 1.604 1.420 1.765 0.7986 0.5216 0.1555 + 19SOL HW2 57 1.502 1.295 1.739 -0.1853 1.1846 0.8074 + 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OW 76 1.446 1.139 0.410 0.1251 0.0937 0.0640 + 26SOL HW1 77 1.392 1.177 0.335 -0.5265 -0.1964 0.3860 + 26SOL HW2 78 1.479 1.048 0.385 2.3550 1.1695 -1.0270 + 27SOL OW 79 1.225 1.804 0.578 0.0688 -0.4596 -0.5400 + 27SOL HW1 80 1.159 1.878 0.589 0.4851 -0.0548 -0.7717 + 27SOL HW2 81 1.184 1.718 0.611 -0.4019 -0.1281 -0.2483 + 28SOL OW 82 1.697 1.262 1.165 0.1584 -0.3131 -0.5006 + 28SOL HW1 83 1.786 1.224 1.190 -0.7016 -2.0596 -0.0291 + 28SOL HW2 84 1.701 1.361 1.170 2.1554 -0.3518 -0.7408 + 29SOL OW 85 0.580 0.785 1.159 0.1576 0.1962 0.7851 + 29SOL HW1 86 0.605 0.804 1.064 -2.4389 0.1562 0.0717 + 29SOL HW2 87 0.537 0.866 1.199 -0.9128 -0.5595 1.1737 + 30SOL OW 88 0.189 1.181 0.903 0.2588 -0.0411 -0.7300 + 30SOL HW1 89 0.275 1.191 0.953 0.5453 0.2862 -1.2794 + 30SOL HW2 90 0.159 1.086 0.908 1.0084 -0.3039 -1.1141 + 31SOL OW 91 0.072 1.404 0.835 -0.1592 -0.0093 -0.8069 + 31SOL HW1 92 0.112 1.314 0.850 1.9460 1.4046 2.7841 + 31SOL HW2 93 -0.022 1.405 0.869 0.0369 -0.6798 -0.2323 + 32SOL OW 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OW 112 0.165 0.204 1.527 0.0532 -0.3656 0.3451 + 38SOL HW1 113 0.107 0.272 1.482 1.6652 0.4666 -0.5055 + 38SOL HW2 114 0.143 0.200 1.625 -1.3666 -0.0031 0.0429 + 39SOL OW 115 1.009 0.126 0.568 0.7018 0.1065 -0.0101 + 39SOL HW1 116 0.948 0.174 0.631 0.7855 -0.2218 0.3236 + 39SOL HW2 117 0.955 0.065 0.510 0.3935 1.8398 -1.5897 + 40SOL OW 118 1.113 1.270 1.544 -0.4074 -0.3083 0.5424 + 40SOL HW1 119 1.181 1.280 1.616 -0.6119 -1.1267 0.8575 + 40SOL HW2 120 1.149 1.211 1.471 -0.5412 -0.2337 0.4157 + 41SOL OW 121 1.840 0.850 1.757 0.0727 0.1798 0.1584 + 41SOL HW1 122 1.772 0.922 1.743 0.6614 0.9018 0.8976 + 41SOL HW2 123 1.932 0.890 1.750 0.4284 -0.8664 -1.2790 + 42SOL OW 124 1.205 0.990 1.178 -0.1756 -0.4886 -0.4219 + 42SOL HW1 125 1.134 0.928 1.142 -1.4368 1.1323 -0.7899 + 42SOL HW2 126 1.267 1.014 1.104 -0.6601 -0.0047 -0.6744 + 43SOL OW 127 1.124 0.665 0.133 0.0693 0.2118 -0.2238 + 43SOL HW1 128 1.071 0.639 0.052 0.5331 -1.9345 0.1390 + 43SOL HW2 129 1.116 0.594 0.202 0.8992 1.3346 1.0482 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b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/ener.edr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/md.log b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/md.log new file mode 100644 index 00000000..0760df4f --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/md.log @@ -0,0 +1,496 @@ +Log file opened on Wed Jan 3 16:24:24 2024 +Host: FAIRmat-AreaC2-Rudzinski pid: 468587 rank ID: 0 number of ranks: 1 + :-) GROMACS - gmx mdrun, 2018.6 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra + Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru + Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus + Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl + Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola + Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov + Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2017, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2018.6 +Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_ENUM_tests/integrator-md/npt-andersen +Command line: + gmx mdrun -s water.tpr -o water.trr + +GROMACS version: 2018.6 +Precision: single +Memory model: 64 bit +MPI library: thread_mpi +OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) +GPU support: OpenCL +SIMD instructions: SSE2 +FFT library: fftw-3.3.8-sse2-avx +RDTSCP usage: disabled +TNG support: enabled +Hwloc support: hwloc-1.11.9 +Tracing support: disabled +Built on: 2019-05-12 20:18:02 +Built by: root@default-0e84dd72-7298-44a4-a670-e10728e370dd [CMAKE] +Build OS/arch: Linux 4.4.0-96-generic x86_64 +Build CPU vendor: Unknown +Build CPU brand: Unknown +Build CPU family: 0 Model: 0 Stepping: 0 +Build CPU features: Unknown +C compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc GNU 7.3.0 +C compiler flags: -msse2 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +C++ compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ GNU 7.3.0 +C++ compiler flags: -msse2 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +OpenCL include dir: /home/jfrudzinski/miniconda3/envs/martignac_2/include +OpenCL library: /home/jfrudzinski/miniconda3/envs/martignac_2/lib/libOpenCL.so +OpenCL version: 2.0 + +NOTE: Detection of GPUs failed. The API reported: + GROMACS cannot run tasks on a GPU. + +Running on 1 node with total 4 cores, 8 logical cores, 0 compatible GPUs +Hardware detected: + CPU info: + Vendor: Intel + Brand: 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz + Family: 6 Model: 140 Stepping: 1 + Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic + Number of AVX-512 FMA units: Cannot run AVX-512 detection - assuming 2 + Hardware topology: Full, with devices + Sockets, cores, and logical processors: + Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] + Numa nodes: + Node 0 (16138244096 bytes mem): 0 1 2 3 4 5 6 7 + Latency: + 0 + 0 1.00 + Caches: + L1: 49152 bytes, linesize 64 bytes, assoc. 12, shared 2 ways + L2: 1310720 bytes, linesize 64 bytes, assoc. 20, shared 2 ways + L3: 12582912 bytes, linesize 64 bytes, assoc. 12, shared 8 ways + PCI devices: + 0000:00:02.0 Id: 8086:9a49 Class: 0x0300 Numa: 0 + 0000:00:0e.0 Id: 8086:9a0b Class: 0x0104 Numa: 0 + 0000:00:14.3 Id: 8086:a0f0 Class: 0x0280 Numa: 0 + 0000:00:1f.6 Id: 8086:15fb Class: 0x0200 Numa: 0 + +Highest SIMD level requested by all nodes in run: AVX_512 +SIMD instructions selected at compile time: SSE2 +This program was compiled for different hardware than you are running on, +which could influence performance. + +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. +Lindahl +GROMACS: High performance molecular simulations through multi-level +parallelism from laptops to supercomputers +SoftwareX 1 (2015) pp. 19-25 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl +Tackling Exascale Software Challenges in Molecular Dynamics Simulations with +GROMACS +In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. +Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl +GROMACS 4.5: a high-throughput and highly parallel open source molecular +simulation toolkit +Bioinformatics 29 (2013) pp. 845-54 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl +GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable +molecular simulation +J. Chem. Theory Comput. 4 (2008) pp. 435-447 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. +Berendsen +GROMACS: Fast, Flexible and Free +J. Comp. Chem. 26 (2005) pp. 1701-1719 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +E. Lindahl and B. Hess and D. van der Spoel +GROMACS 3.0: A package for molecular simulation and trajectory analysis +J. Mol. Mod. 7 (2001) pp. 306-317 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +H. J. C. Berendsen, D. van der Spoel and R. van Drunen +GROMACS: A message-passing parallel molecular dynamics implementation +Comp. Phys. Comm. 91 (1995) pp. 43-56 +-------- -------- --- Thank You --- -------- -------- + +Input Parameters: + integrator = md + tinit = 0 + dt = 0.001 + nsteps = 1 + init-step = 0 + simulation-part = 1 + comm-mode = Linear + nstcomm = 1 + bd-fric = 0 + ld-seed = -1591423791 + emtol = 10 + emstep = 0.01 + niter = 20 + fcstep = 0 + nstcgsteep = 1000 + nbfgscorr = 10 + rtpi = 0.05 + nstxout = 1 + nstvout = 1 + nstfout = 1 + nstlog = 1 + nstcalcenergy = 1 + nstenergy = 1 + nstxout-compressed = 0 + compressed-x-precision = 1000 + cutoff-scheme = Verlet + nstlist = 1 + ns-type = Grid + pbc = xyz + periodic-molecules = false + verlet-buffer-tolerance = 0.005 + rlist = 0.9 + coulombtype = PME + coulomb-modifier = Potential-shift + rcoulomb-switch = 0 + rcoulomb = 0.9 + epsilon-r = 1 + epsilon-rf = inf + vdw-type = Cut-off + vdw-modifier = Potential-shift + rvdw-switch = 0 + rvdw = 0.9 + DispCorr = EnerPres + table-extension = 1 + fourierspacing = 0.08 + fourier-nx = 24 + fourier-ny = 24 + fourier-nz = 24 + pme-order = 6 + ewald-rtol = 1e-06 + ewald-rtol-lj = 0.001 + lj-pme-comb-rule = Geometric + ewald-geometry = 0 + epsilon-surface = 0 + implicit-solvent = No + gb-algorithm = Still + nstgbradii = 1 + rgbradii = 1 + gb-epsilon-solvent = 80 + gb-saltconc = 0 + gb-obc-alpha = 1 + gb-obc-beta = 0.8 + gb-obc-gamma = 4.85 + gb-dielectric-offset = 0.009 + sa-algorithm = Ace-approximation + sa-surface-tension = 2.05016 + tcoupl = Nose-Hoover + nsttcouple = 1 + nh-chain-length = 1 + print-nose-hoover-chain-variables = false + pcoupl = Parrinello-Rahman + pcoupltype = Isotropic + nstpcouple = 1 + tau-p = 5 + compressibility (3x3): + compressibility[ 0]={ 7.40000e-05, 0.00000e+00, 0.00000e+00} + compressibility[ 1]={ 0.00000e+00, 7.40000e-05, 0.00000e+00} + compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 7.40000e-05} + ref-p (3x3): + ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} + ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} + refcoord-scaling = No + posres-com (3): + posres-com[0]= 0.00000e+00 + posres-com[1]= 0.00000e+00 + posres-com[2]= 0.00000e+00 + posres-comB (3): + posres-comB[0]= 0.00000e+00 + posres-comB[1]= 0.00000e+00 + posres-comB[2]= 0.00000e+00 + QMMM = false + QMconstraints = 0 + QMMMscheme = 0 + MMChargeScaleFactor = 1 +qm-opts: + ngQM = 0 + constraint-algorithm = Lincs + continuation = false + Shake-SOR = false + shake-tol = 0.0001 + lincs-order = 4 + lincs-iter = 1 + lincs-warnangle = 30 + nwall = 0 + wall-type = 9-3 + wall-r-linpot = -1 + wall-atomtype[0] = -1 + wall-atomtype[1] = -1 + wall-density[0] = 0 + wall-density[1] = 0 + wall-ewald-zfac = 3 + pull = false + awh = false + rotation = false + interactiveMD = false + disre = No + disre-weighting = Conservative + disre-mixed = false + dr-fc = 1000 + dr-tau = 0 + nstdisreout = 100 + orire-fc = 0 + orire-tau = 0 + nstorireout = 100 + free-energy = no + cos-acceleration = 0 + deform (3x3): + deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + simulated-tempering = false + swapcoords = no + userint1 = 0 + userint2 = 0 + userint3 = 0 + userint4 = 0 + userreal1 = 0 + userreal2 = 0 + userreal3 = 0 + userreal4 = 0 + applied-forces: + electric-field: + x: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + y: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + z: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 +grpopts: + nrdf: 1293 + ref-t: 298 + tau-t: 0.5 +annealing: No +annealing-npoints: 0 + acc: 0 0 0 + nfreeze: N N N + energygrp-flags[ 0]: 0 + + +Using 1 MPI thread +Using 8 OpenMP threads + +Pinning threads with an auto-selected logical core stride of 1 +System total charge: 0.000 +Will do PME sum in reciprocal space for electrostatic interactions. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen +A smooth particle mesh Ewald method +J. Chem. Phys. 103 (1995) pp. 8577-8592 +-------- -------- --- Thank You --- -------- -------- + +Using a Gaussian width (1/beta) of 0.260197 nm for Ewald +Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-06 +Initialized non-bonded Ewald correction tables, spacing: 8.41e-04 size: 1071 + +Long Range LJ corr.: 2.9078e-04 +Generated table with 950 data points for Ewald. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ6. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ12. +Tabscale = 500 points/nm + +Using SIMD 4x4 nonbonded short-range kernels + +Using a 4x4 pair-list setup: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm +At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm + +Using geometric Lennard-Jones combination rule + +Removing pbc first time + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Miyamoto and P. A. Kollman +SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid +Water Models +J. Comp. Chem. 13 (1992) pp. 952-962 +-------- -------- --- Thank You --- -------- -------- + + +Intra-simulation communication will occur every 1 steps. +Center of mass motion removal mode is Linear +We have the following groups for center of mass motion removal: + 0: rest +There are: 648 Atoms + +Constraining the starting coordinates (step 0) + +Constraining the coordinates at t0-dt (step 0) +RMS relative constraint deviation after constraining: 0.00e+00 +Initial temperature: 303.778 K + +Started mdrun on rank 0 Wed Jan 3 16:24:25 2024 + Step Time + 0 0.00000 + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.98181e+03 -1.08747e+02 -1.21912e+04 1.28385e+02 -1.01898e+04 + Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) + 1.63225e+03 -8.55751e+03 -8.55712e+03 3.03657e+02 -2.80811e+02 + Pressure (bar) + -4.80368e+02 + + Step Time + 1 0.00100 + +Writing checkpoint, step 1 at Wed Jan 3 16:24:25 2024 + + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97589e+03 -1.08747e+02 -1.21828e+04 1.28145e+02 -1.01875e+04 + Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) + 1.62999e+03 -8.55753e+03 -8.55712e+03 3.03236e+02 -2.80811e+02 + Pressure (bar) + -5.21850e+02 + + <====== ############### ==> + <==== A V E R A G E S ====> + <== ############### ======> + + Statistics over 2 steps using 2 frames + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97885e+03 -1.08747e+02 -1.21870e+04 1.28265e+02 -1.01886e+04 + Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) + 1.63112e+03 -8.55752e+03 -8.55712e+03 3.03447e+02 -2.80811e+02 + Pressure (bar) + -5.01109e+02 + + Box-X Box-Y Box-Z + 1.86060e+00 1.86060e+00 1.86060e+00 + + Total Virial (kJ/mol) + 6.67950e+02 1.09538e+02 1.75949e+02 + 1.09305e+02 5.41446e+02 -2.28119e+01 + 1.76313e+02 -2.26614e+01 7.13286e+02 + + Pressure (bar) + -7.99493e+02 -4.57999e+02 -9.59805e+02 + -4.56798e+02 2.20487e+02 6.28021e+01 + -9.61681e+02 6.20258e+01 -9.24321e+02 + + + M E G A - F L O P S A C C O U N T I N G + + NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels + RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table + W3=SPC/TIP3p W4=TIP4p (single or pairs) + V&F=Potential and force V=Potential only F=Force only + + Computing: M-Number M-Flops % Flops +----------------------------------------------------------------------------- + Pair Search distance check 0.306406 2.758 8.6 + NxN QSTab Elec. + LJ [V&F] 0.207760 12.258 38.2 + NxN QSTab Elec. [V&F] 0.198560 8.141 25.3 + Calc Weights 0.003888 0.140 0.4 + Spread Q Bspline 0.279936 0.560 1.7 + Gather F Bspline 0.279936 1.680 5.2 + 3D-FFT 0.760588 6.085 18.9 + Solve PME 0.001152 0.074 0.2 + Shift-X 0.001296 0.008 0.0 + Virial 0.001386 0.025 0.1 + Stop-CM 0.001944 0.019 0.1 + Calc-Ekin 0.001944 0.052 0.2 + Constraint-V 0.001944 0.016 0.0 + Constraint-Vir 0.001296 0.031 0.1 + Settle 0.000864 0.279 0.9 +----------------------------------------------------------------------------- + Total 32.125 100.0 +----------------------------------------------------------------------------- + + + R E A L C Y C L E A N D T I M E A C C O U N T I N G + +On 1 MPI rank, each using 8 OpenMP threads + + Computing: Num Num Call Wall time Giga-Cycles + Ranks Threads Count (s) total sum % +----------------------------------------------------------------------------- + Neighbor search 1 8 2 0.002 0.034 6.5 + Force 1 8 2 0.000 0.004 0.8 + PME mesh 1 8 2 0.000 0.006 1.1 + NB X/F buffer ops. 1 8 2 0.000 0.000 0.0 + Write traj. 1 8 2 0.016 0.228 43.9 + Update 1 8 2 0.001 0.011 2.1 + Constraints 1 8 2 0.000 0.000 0.1 + Rest 0.016 0.236 45.5 +----------------------------------------------------------------------------- + Total 0.036 0.520 100.0 +----------------------------------------------------------------------------- + Breakdown of PME mesh computation +----------------------------------------------------------------------------- + PME spread 1 8 2 0.000 0.002 0.4 + PME gather 1 8 2 0.000 0.002 0.3 + PME 3D-FFT 1 8 4 0.000 0.001 0.2 + PME solve Elec 1 8 2 0.000 0.001 0.1 +----------------------------------------------------------------------------- + + Core t (s) Wall t (s) (%) + Time: 0.288 0.036 800.0 + (ns/day) (hour/ns) +Performance: 4.803 4.997 +Finished mdrun on rank 0 Wed Jan 3 16:24:25 2024 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/mdout.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/mdout.mdp new file mode 100644 index 00000000..e6ae6b70 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/mdout.mdp @@ -0,0 +1,353 @@ +; +; File 'mdout.mdp' was generated +; By user: jfrudzinski (1000) +; On host: FAIRmat-AreaC2-Rudzinski +; At date: Wed Jan 3 16:24:24 2024 +; +; Created by: +; :-) GROMACS - gmx grompp, 2018.6 (-: +; +; Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +; Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +; Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_ENUM_tests/integrator-md/npt-andersen +; Command line: +; gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +; VARIOUS PREPROCESSING OPTIONS +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/roe +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ +; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) +define = + +; RUN CONTROL PARAMETERS +integrator = md +; Start time and timestep in ps +tinit = 0.0 +dt = 0.001 +nsteps = 1 +; For exact run continuation or redoing part of a run +init-step = 0 +; Part index is updated automatically on checkpointing (keeps files separate) +simulation-part = 1 +; mode for center of mass motion removal +comm-mode = linear +; number of steps for center of mass motion removal +nstcomm = 1 +; group(s) for center of mass motion removal +comm-grps = + +; LANGEVIN DYNAMICS OPTIONS +; Friction coefficient (amu/ps) and random seed +bd-fric = 0 +ld-seed = -1 + +; ENERGY MINIMIZATION OPTIONS +; Force tolerance and initial step-size +emtol = 10 +emstep = 0.01 +; Max number of iterations in relax-shells +niter = 20 +; Step size (ps^2) for minimization of flexible constraints +fcstep = 0 +; Frequency of steepest descents steps when doing CG +nstcgsteep = 1000 +nbfgscorr = 10 + +; TEST PARTICLE INSERTION OPTIONS +rtpi = 0.05 + +; OUTPUT CONTROL OPTIONS +; Output frequency for coords (x), velocities (v) and forces (f) +nstxout = 1 +nstvout = 1 +nstfout = 1 +; Output frequency for energies to log file and energy file +nstlog = 1 +nstcalcenergy = 100 +nstenergy = 1 +; Output frequency and precision for .xtc file +nstxout-compressed = 0 +compressed-x-precision = 1000 +; This selects the subset of atoms for the compressed +; trajectory file. You can select multiple groups. By +; default, all atoms will be written. +compressed-x-grps = +; Selection of energy groups +energygrps = System + +; NEIGHBORSEARCHING PARAMETERS +; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) +cutoff-scheme = Verlet +; nblist update frequency +nstlist = 1 +; ns algorithm (simple or grid) +ns_type = grid +; Periodic boundary conditions: xyz, no, xy +pbc = xyz +periodic-molecules = no +; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, +; a value of -1 means: use rlist +verlet-buffer-tolerance = 0.005 +; nblist cut-off +rlist = 0.9 +; long-range cut-off for switched potentials + +; OPTIONS FOR ELECTROSTATICS AND VDW +; Method for doing electrostatics +coulombtype = PME +coulomb-modifier = Potential-shift-Verlet +rcoulomb-switch = 0 +rcoulomb = 0.9 +; Relative dielectric constant for the medium and the reaction field +epsilon-r = 1 +epsilon-rf = 0 +; Method for doing Van der Waals +vdwtype = cutoff +vdw-modifier = Potential-shift-Verlet +; cut-off lengths +rvdw-switch = 0 +rvdw = 0.9 +; Apply long range dispersion corrections for Energy and Pressure +DispCorr = EnerPres +; Extension of the potential lookup tables beyond the cut-off +table-extension = 1 +; Separate tables between energy group pairs +energygrp-table = +; Spacing for the PME/PPPM FFT grid +fourierspacing = 0.08 +; FFT grid size, when a value is 0 fourierspacing will be used +fourier-nx = 0 +fourier-ny = 0 +fourier-nz = 0 +; EWALD/PME/PPPM parameters +pme_order = 6 +ewald_rtol = 1e-06 +ewald-rtol-lj = 0.001 +lj-pme-comb-rule = Geometric +ewald-geometry = 3d +epsilon-surface = 0 + +; IMPLICIT SOLVENT ALGORITHM +implicit-solvent = No + +; GENERALIZED BORN ELECTROSTATICS +; Algorithm for calculating Born radii +gb-algorithm = Still +; Frequency of calculating the Born radii inside rlist +nstgbradii = 1 +; Cutoff for Born radii calculation; the contribution from atoms +; between rlist and rgbradii is updated every nstlist steps +rgbradii = 1 +; Dielectric coefficient of the implicit solvent +gb-epsilon-solvent = 80 +; Salt concentration in M for Generalized Born models +gb-saltconc = 0 +; Scaling factors used in the OBC GB model. Default values are OBC(II) +gb-obc-alpha = 1 +gb-obc-beta = 0.8 +gb-obc-gamma = 4.85 +gb-dielectric-offset = 0.009 +sa-algorithm = Ace-approximation +; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA +; The value -1 will set default value for Still/HCT/OBC GB-models. +sa-surface-tension = -1 + +; OPTIONS FOR WEAK COUPLING ALGORITHMS +; Temperature coupling +tcoupl = nose-hoover +nsttcouple = -1 +nh-chain-length = 10 +print-nose-hoover-chain-variables = no +; Groups to couple separately +tc_grps = System +; Time constant (ps) and reference temperature (K) +tau_t = 0.5 +ref_t = 298 +; pressure coupling +pcoupl = Parrinello-Rahman +pcoupltype = Isotropic +nstpcouple = -1 +; Time constant (ps), compressibility (1/bar) and reference P (bar) +tau-p = 5.0 +compressibility = 7.4e-5 +ref-p = 1.0 +; Scaling of reference coordinates, No, All or COM +refcoord-scaling = No + +; OPTIONS FOR QMMM calculations +QMMM = no +; Groups treated Quantum Mechanically +QMMM-grps = +; QM method +QMmethod = +; QMMM scheme +QMMMscheme = normal +; QM basisset +QMbasis = +; QM charge +QMcharge = +; QM multiplicity +QMmult = +; Surface Hopping +SH = +; CAS space options +CASorbitals = +CASelectrons = +SAon = +SAoff = +SAsteps = +; Scale factor for MM charges +MMChargeScaleFactor = 1 + +; SIMULATED ANNEALING +; Type of annealing for each temperature group (no/single/periodic) +annealing = +; Number of time points to use for specifying annealing in each group +annealing-npoints = +; List of times at the annealing points for each group +annealing-time = +; Temp. at each annealing point, for each group. +annealing-temp = + +; GENERATE VELOCITIES FOR STARTUP RUN +gen-vel = no +gen-temp = 300 +gen-seed = -1 + +; OPTIONS FOR BONDS +constraints = none +; Type of constraint algorithm +constraint-algorithm = Lincs +; Do not constrain the start configuration +continuation = no +; Use successive overrelaxation to reduce the number of shake iterations +Shake-SOR = no +; Relative tolerance of shake +shake-tol = 0.0001 +; Highest order in the expansion of the constraint coupling matrix +lincs-order = 4 +; Number of iterations in the final step of LINCS. 1 is fine for +; normal simulations, but use 2 to conserve energy in NVE runs. +; For energy minimization with constraints it should be 4 to 8. +lincs-iter = 1 +; Lincs will write a warning to the stderr if in one step a bond +; rotates over more degrees than +lincs-warnangle = 30 +; Convert harmonic bonds to morse potentials +morse = no + +; ENERGY GROUP EXCLUSIONS +; Pairs of energy groups for which all non-bonded interactions are excluded +energygrp-excl = + +; WALLS +; Number of walls, type, atom types, densities and box-z scale factor for Ewald +nwall = 0 +wall-type = 9-3 +wall-r-linpot = -1 +wall-atomtype = +wall-density = +wall-ewald-zfac = 3 + +; COM PULLING +pull = no + +; AWH biasing +awh = no + +; ENFORCED ROTATION +; Enforced rotation: No or Yes +rotation = no + +; Group to display and/or manipulate in interactive MD session +IMD-group = + +; NMR refinement stuff +; Distance restraints type: No, Simple or Ensemble +disre = No +; Force weighting of pairs in one distance restraint: Conservative or Equal +disre-weighting = Conservative +; Use sqrt of the time averaged times the instantaneous violation +disre-mixed = no +disre-fc = 1000 +disre-tau = 0 +; Output frequency for pair distances to energy file +nstdisreout = 100 +; Orientation restraints: No or Yes +orire = no +; Orientation restraints force constant and tau for time averaging +orire-fc = 0 +orire-tau = 0 +orire-fitgrp = +; Output frequency for trace(SD) and S to energy file +nstorireout = 100 + +; Free energy variables +free-energy = no +couple-moltype = +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q +couple-intramol = no +init-lambda = -1 +init-lambda-state = -1 +delta-lambda = 0 +nstdhdl = 50 +fep-lambdas = +mass-lambdas = +coul-lambdas = +vdw-lambdas = +bonded-lambdas = +restraint-lambdas = +temperature-lambdas = +calc-lambda-neighbors = 1 +init-lambda-weights = +dhdl-print-energy = no +sc-alpha = 0 +sc-power = 1 +sc-r-power = 6 +sc-sigma = 0.3 +sc-coul = no +separate-dhdl-file = yes +dhdl-derivatives = yes +dh_hist_size = 0 +dh_hist_spacing = 0.1 + +; Non-equilibrium MD stuff +acc-grps = +accelerate = +freezegrps = +freezedim = +cos-acceleration = 0 +deform = + +; simulated tempering variables +simulated-tempering = no +simulated-tempering-scaling = geometric +sim-temp-low = 300 +sim-temp-high = 300 + +; Ion/water position swapping for computational electrophysiology setups +; Swap positions along direction: no, X, Y, Z +swapcoords = no +adress = no + +; User defined thingies +user1-grps = +user2-grps = +userint1 = 0 +userint2 = 0 +userint3 = 0 +userint4 = 0 +userreal1 = 0 +userreal2 = 0 +userreal3 = 0 +userreal4 = 0 +; Electric fields +; Format for electric-field-x, etc. is: four real variables: +; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), +; and sigma (ps) width of the pulse. Omega = 0 means static field, +; sigma = 0 means no pulse, leaving the field to be a cosine function. +electric-field-x = 0 0 0 0 +electric-field-y = 0 0 0 0 +electric-field-z = 0 0 0 0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/state.cpt b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/state.cpt new file mode 100644 index 00000000..209c6e9c Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/state.cpt differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.298.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.298.mdp new file mode 100644 index 00000000..06ebd021 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.298.mdp @@ -0,0 +1,52 @@ +; Preprocessing +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ + +; Run Control +integrator = md +tinit = 0.0 +dt = 0.001 ; 1.0 fs +nsteps = 1 ; 20 ns +nstcomm = 1 ; no. steps between removing com motion +comm-mode = linear ; remove com translation + +; Output Control +nstxout = 1 ; no. steps between printing coords to trr file => 1ps +nstvout = 1 ; no. steps between printing veloc to trr file +nstfout = 1 ; no. steps between printing forces to trr file => 1ps +nstlog = 1 ; no. steps between printing energy to log file => 1ps +nstenergy = 1 ; no. steps between printing energy to edr file => 1ps +nstxtcout = 0 ; no. stpes between printing coords to xtc file +energygrps = System ; groups for writing energy file + +; Neighbor searching +nstlist = 1 ; update neighbor list every step +ns_type = grid ; check neighbor list using grid +rlist = 0.9 ; cutoff distance (nm) for short-range neighbor list + +; Electrostatics and VdW +coulombtype = PME ; fast particle-mesh ewald electrostatics +rcoulomb = 0.9 ; distance for the Coulomb cut-off +vdwtype = cutoff ; truncated LJ interactions +rvdw = 0.9 ; distance for LJ cut-off +DispCorr = EnerPres ; apply long range disp. correct. for Energy/Pres +fourierspacing = 0.08 ; max grid spacing fr FFT grid in PME +pme_order = 6 ; interpolation order for PME +ewald_rtol = 1e-06 ; relative strength of direct potential at cutoff +optimize_fft = yes ; optimize fft_grids + +; Temperature Coupling +tcoupl = nose-hoover ; nose-hoover for correct ensemble +tc_grps = System ; groups to couple separtly to temp. bath +tau_t = 0.5 ; time constant for coupling +ref_t = 298 ; ref. temperature for coupling + +; Velocity generation +;gen_vel = yes ; generate velocities with Max. dist. +;gen_temp = 298 ; temp. for Max. dist. +;gen_seed = 173529 ; for random number generator + +; Pressure coupling +pcoupl = Parrinello-Rahman +tau-p = 5.0 +compressibility = 7.4e-5 +ref-p = 1.0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.confout.gro new file mode 100644 index 00000000..0244d504 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.427 0.087 1.634 0.0670 0.6261 -0.3260 + 1SOL HW1 2 0.352 0.153 1.636 -0.6525 -0.2083 0.2628 + 1SOL HW2 3 0.394 -0.001 1.600 1.0005 0.5272 -1.0056 + 2SOL OW 4 0.365 0.990 0.648 0.2321 -0.9063 -0.2980 + 2SOL HW1 5 0.377 0.914 0.584 -0.7093 -1.6057 0.3416 + 2SOL HW2 6 0.274 1.030 0.635 -0.0303 -1.1620 0.7020 + 3SOL OW 7 1.293 1.628 1.682 0.0780 0.2611 -0.6033 + 3SOL HW1 8 1.334 1.698 1.741 0.7308 -0.2019 -0.4969 + 3SOL HW2 9 1.365 1.565 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505 0.830 0.328 0.586 0.4046 -0.2408 0.4182 + 169SOL HW1 506 0.814 0.426 0.572 1.0997 0.0252 1.4337 + 169SOL HW2 507 0.793 0.300 0.674 0.2024 -0.9005 0.1273 + 170SOL OW 508 1.831 1.624 0.059 0.3766 0.4513 -0.0063 + 170SOL HW1 509 1.926 1.599 0.041 -0.2526 -1.2869 -1.0429 + 170SOL HW2 510 1.784 1.548 0.104 -0.9708 0.6468 -1.0362 + 171SOL OW 511 1.114 0.420 0.512 -0.4071 0.1354 0.1636 + 171SOL HW1 512 1.031 0.379 0.550 -0.5249 -1.0053 -1.3043 + 171SOL HW2 513 1.139 0.500 0.566 -2.4272 0.4440 0.6733 + 172SOL OW 514 1.612 0.142 0.124 0.0310 -0.0285 -0.1944 + 172SOL HW1 515 1.638 0.221 0.069 0.1622 -0.0386 -0.1486 + 172SOL HW2 516 1.618 0.165 0.221 -0.3003 0.0203 -0.1855 + 173SOL OW 517 1.273 0.744 1.581 0.0598 0.1595 -0.3661 + 173SOL HW1 518 1.290 0.674 1.512 0.9810 -0.6546 0.6832 + 173SOL HW2 519 1.177 0.773 1.576 -0.3405 -1.2113 -0.7504 + 174SOL OW 520 0.842 1.471 0.029 0.6270 -0.6247 0.3077 + 174SOL HW1 521 0.782 1.527 0.086 -0.7781 -1.4610 -0.3123 + 174SOL HW2 522 0.915 1.528 -0.008 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180SOL HW2 540 0.235 1.499 0.857 0.6896 -1.4571 -1.3748 + 181SOL OW 541 1.370 0.007 0.942 0.3182 -0.3568 -0.3435 + 181SOL HW1 542 1.432 -0.071 0.940 0.0645 -0.5854 0.5377 + 181SOL HW2 543 1.282 -0.018 0.902 -0.8327 -1.4792 2.7400 + 182SOL OW 544 0.253 0.428 0.457 -0.0183 0.3143 0.3329 + 182SOL HW1 545 0.311 0.351 0.430 -0.1553 1.1020 -2.4236 + 182SOL HW2 546 0.170 0.393 0.502 1.6909 -0.9043 2.6201 + 183SOL OW 547 0.286 0.097 1.177 0.5078 -0.0262 -0.1346 + 183SOL HW1 548 0.219 0.171 1.184 -0.0027 -0.3660 -1.2136 + 183SOL HW2 549 0.367 0.130 1.128 1.1385 0.3882 1.1809 + 184SOL OW 550 0.025 1.844 1.398 0.8241 0.0883 -0.4432 + 184SOL HW1 551 0.099 1.895 1.442 1.8365 -1.9952 0.2967 + 184SOL HW2 552 -0.012 1.776 1.461 -0.4736 -0.1561 -1.4373 + 185SOL OW 553 0.534 0.658 1.575 -0.3340 0.3639 -0.0368 + 185SOL HW1 554 0.574 0.664 1.667 0.3355 -1.0454 -0.2294 + 185SOL HW2 555 0.607 0.657 1.507 -0.6335 -2.9360 -0.3589 + 186SOL OW 556 1.418 0.775 0.820 -0.0169 1.0421 -0.8445 + 186SOL HW1 557 1.378 0.691 0.857 0.7531 1.3106 0.6462 + 186SOL HW2 558 1.398 0.782 0.723 -0.6095 -0.5640 -0.8452 + 187SOL OW 559 0.222 0.944 1.345 -0.2158 0.3297 -0.7016 + 187SOL HW1 560 0.131 0.904 1.335 -0.6758 0.9556 0.9203 + 187SOL HW2 561 0.226 0.999 1.428 1.2918 1.2851 -1.3770 + 188SOL OW 562 0.914 0.467 0.189 0.6525 0.6939 0.0840 + 188SOL HW1 563 0.871 0.549 0.227 -0.0617 0.1423 0.4674 + 188SOL HW2 564 0.873 0.447 0.100 0.4158 0.4051 0.2610 + 189SOL OW 565 0.801 1.764 1.597 0.0175 0.4390 0.1863 + 189SOL HW1 566 0.751 1.834 1.649 1.3774 1.6958 -0.1520 + 189SOL HW2 567 0.872 1.724 1.655 -0.2129 -0.0604 0.1199 + 190SOL OW 568 0.833 0.451 1.539 0.1980 0.3304 0.0083 + 190SOL HW1 569 0.803 0.547 1.533 -0.8407 0.1465 1.8404 + 190SOL HW2 570 0.929 0.444 1.510 0.6995 2.1522 1.1685 + 191SOL OW 571 1.110 0.916 0.220 0.1476 0.5001 -0.4889 + 191SOL HW1 572 1.129 0.820 0.200 -2.6997 0.4489 -3.4273 + 191SOL HW2 573 1.019 0.923 0.262 1.1175 1.7959 1.4857 + 192SOL OW 574 0.996 0.056 1.146 -0.0994 0.5545 0.4537 + 192SOL HW1 575 0.972 -0.004 1.222 -0.6136 1.3158 0.8946 + 192SOL HW2 576 0.960 0.148 1.162 1.8146 1.3433 0.4012 + 193SOL OW 577 0.514 1.254 1.408 0.1676 0.1755 -0.1092 + 193SOL HW1 578 0.528 1.208 1.496 -1.3291 -0.5253 -0.2132 + 193SOL HW2 579 0.601 1.288 1.374 0.7114 0.8100 1.8430 + 194SOL OW 580 1.424 1.837 1.808 0.0919 -0.5746 -0.2857 + 194SOL HW1 581 1.486 1.823 1.731 0.4877 1.9227 -0.4851 + 194SOL HW2 582 1.478 1.861 1.889 -0.4948 0.0238 -0.0653 + 195SOL OW 583 0.658 1.239 0.620 -0.3609 0.5478 -0.5495 + 195SOL HW1 584 0.747 1.197 0.604 -0.5919 0.8796 -2.7776 + 195SOL HW2 585 0.604 1.180 0.680 0.7884 -0.3959 -0.4194 + 196SOL OW 586 1.379 0.250 1.783 0.0082 -0.7042 0.3366 + 196SOL HW1 587 1.419 0.159 1.771 2.8172 0.8867 -3.3603 + 196SOL HW2 588 1.436 0.303 1.846 -0.5107 -0.8573 0.9364 + 197SOL OW 589 1.406 0.936 0.182 0.4528 -0.1813 0.0754 + 197SOL HW1 590 1.402 0.861 0.116 0.2006 -1.4207 1.4793 + 197SOL HW2 591 1.314 0.957 0.216 0.8623 -1.2400 1.8888 + 198SOL OW 592 0.030 0.412 1.436 0.2007 -0.0565 -0.4994 + 198SOL HW1 593 0.098 0.476 1.400 -0.3590 1.3329 0.8709 + 198SOL HW2 594 -0.018 0.453 1.513 -1.5666 -1.3714 -0.8498 + 199SOL OW 595 0.013 1.493 0.579 -0.5266 -0.7272 0.0410 + 199SOL HW1 596 0.039 1.479 0.675 -1.1788 1.6396 0.5768 + 199SOL HW2 597 -0.078 1.455 0.563 -1.3122 0.7763 0.8986 + 200SOL OW 598 0.446 0.239 1.024 0.0321 -0.2285 0.0174 + 200SOL HW1 599 0.426 0.256 0.928 -0.6769 0.6990 0.3210 + 200SOL HW2 600 0.440 0.325 1.075 1.7030 -0.4725 0.6645 + 201SOL OW 601 0.389 0.194 0.371 0.3108 -0.2167 0.5535 + 201SOL HW1 602 0.390 0.206 0.272 -0.3545 0.4874 0.6282 + 201SOL HW2 603 0.331 0.115 0.394 0.0047 -0.0376 0.4087 + 202SOL OW 604 0.672 1.424 0.815 -0.5655 0.8860 -0.1168 + 202SOL HW1 605 0.659 1.346 0.753 1.9136 -0.9085 1.5104 + 202SOL HW2 606 0.730 1.492 0.770 -0.6763 0.6517 -0.6213 + 203SOL OW 607 0.088 0.919 0.941 0.4703 0.3888 0.1022 + 203SOL HW1 608 0.118 0.832 0.980 -0.9147 -0.1690 -0.0698 + 203SOL HW2 609 -0.006 0.938 0.969 1.1561 2.4272 1.1431 + 204SOL OW 610 1.613 1.447 0.506 -0.2397 0.1224 -0.4911 + 204SOL HW1 611 1.574 1.455 0.414 -0.6147 -2.1473 -0.5397 + 204SOL HW2 612 1.539 1.443 0.573 0.0323 3.0606 0.0867 + 205SOL OW 613 1.801 1.172 1.523 -0.1389 0.0380 0.7452 + 205SOL HW1 614 1.813 1.262 1.566 -0.0595 0.0259 0.7478 + 205SOL HW2 615 1.830 1.176 1.427 -1.0958 0.2748 0.4670 + 206SOL OW 616 1.671 1.161 0.622 0.0381 -0.1968 -0.8982 + 206SOL HW1 617 1.659 1.062 0.624 1.0081 -0.2945 0.2200 + 206SOL HW2 618 1.665 1.194 0.528 -3.4793 -0.9138 -0.9865 + 207SOL OW 619 0.744 0.684 1.371 -0.4972 -0.4176 0.1462 + 207SOL HW1 620 0.819 0.647 1.316 -0.8700 -0.5741 -0.2655 + 207SOL HW2 621 0.664 0.697 1.313 -0.0811 1.9892 0.0593 + 208SOL OW 622 0.821 0.317 1.194 0.4536 0.4539 -0.3308 + 208SOL HW1 623 0.766 0.361 1.123 1.4276 0.6847 -0.9606 + 208SOL HW2 624 0.768 0.311 1.279 -0.1401 1.6828 -0.6050 + 209SOL OW 625 1.664 1.037 1.689 -0.3971 0.4743 0.3950 + 209SOL HW1 626 1.571 1.024 1.655 -0.4077 -0.2767 0.7076 + 209SOL HW2 627 1.711 1.105 1.632 -0.9022 0.3384 -0.1894 + 210SOL OW 628 1.819 0.231 0.807 -0.1924 0.5243 -0.1692 + 210SOL HW1 629 1.852 0.144 0.844 1.0633 0.7808 -0.6607 + 210SOL HW2 630 1.720 0.239 0.823 0.0839 0.0674 2.0047 + 211SOL OW 631 0.979 1.242 0.144 -0.2018 0.2018 -0.0354 + 211SOL HW1 632 0.938 1.316 0.090 -0.6232 -0.6929 -0.9633 + 211SOL HW2 633 0.946 1.247 0.238 -0.1197 1.2714 -0.0561 + 212SOL OW 634 0.778 0.948 0.748 0.5845 0.0149 -0.7815 + 212SOL HW1 635 0.818 1.006 0.676 -0.1841 1.1423 -0.3163 + 212SOL HW2 636 0.695 0.991 0.783 1.4375 -0.0808 1.4255 + 213SOL OW 637 1.814 1.673 1.613 -0.0991 0.5855 0.0909 + 213SOL HW1 638 1.826 1.683 1.712 0.1001 -0.7483 0.2122 + 213SOL HW2 639 1.873 1.599 1.580 -0.2204 0.9765 -1.0148 + 214SOL OW 640 0.068 1.175 1.260 0.2612 0.5460 0.5693 + 214SOL HW1 641 0.147 1.235 1.273 0.1725 0.8319 -0.1693 + 214SOL HW2 642 0.100 1.081 1.245 0.4518 0.6382 0.3995 + 215SOL OW 643 1.089 0.245 0.891 -0.1119 0.5785 0.4751 + 215SOL HW1 644 0.994 0.267 0.866 -0.3021 -0.0338 0.6459 + 215SOL HW2 645 1.099 0.146 0.898 0.6144 0.6299 0.1871 + 216SOL OW 646 1.135 1.550 0.658 0.1441 0.6409 -0.1721 + 216SOL HW1 647 1.078 1.522 0.736 0.3615 1.9482 0.4795 + 216SOL HW2 648 1.131 1.480 0.587 0.5499 -0.9515 1.3195 + 1.86060 1.86060 1.86060 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.top b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.top new file mode 100644 index 00000000..132cf50f --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.top @@ -0,0 +1,16 @@ +; +; +; Topology file for spce water +; +; +; +#include "oplsaa.ff/forcefield.itp" + +#include "oplsaa.ff/spce.itp" + +[ system ] +spce water + +[ molecules ] +SOL 216 + diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.tpr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.tpr new file mode 100644 index 00000000..74cdc03b Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.tpr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.trr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.trr new file mode 100644 index 00000000..0a45d29c Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/water.trr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/commands.sh b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/commands.sh new file mode 100755 index 00000000..2e31bc08 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/commands.sh @@ -0,0 +1,3 @@ +gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +gmx mdrun -s water.tpr -o water.trr diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/confout.gro new file mode 100644 index 00000000..7389fd5d --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.427 0.088 1.634 0.0798 0.6251 -0.3197 + 1SOL HW1 2 0.351 0.152 1.636 -0.7154 -0.3156 0.2598 + 1SOL HW2 3 0.395 -0.000 1.599 1.0654 0.4170 -0.7312 + 2SOL OW 4 0.365 0.989 0.648 0.2274 -0.9312 -0.3081 + 2SOL HW1 5 0.376 0.912 0.585 -0.7194 -1.6604 0.3933 + 2SOL HW2 6 0.274 1.029 0.636 -0.0767 -1.2794 0.8160 + 3SOL OW 7 1.293 1.628 1.681 0.0957 0.2473 -0.5794 + 3SOL HW1 8 1.334 1.698 1.741 0.8081 -0.3745 -0.3390 + 3SOL HW2 9 1.364 1.565 1.650 -0.4448 -0.0000 -1.3067 + 4SOL OW 10 0.922 1.027 1.587 -0.3808 -0.1014 0.3892 + 4SOL HW1 11 0.949 1.121 1.566 0.9941 -0.5016 0.3561 + 4SOL HW2 12 0.938 1.009 1.684 -0.3768 -0.3928 0.3354 + 5SOL OW 13 0.870 1.326 0.395 -0.6481 0.2651 0.0675 + 5SOL HW1 14 0.954 1.366 0.434 -0.8065 -1.2117 1.9781 + 5SOL HW2 15 0.792 1.382 0.421 -0.4609 0.7081 -0.3073 + 6SOL OW 16 0.300 0.862 0.125 -0.1236 -0.5479 0.6540 + 6SOL HW1 17 0.251 0.909 0.051 -1.0810 1.0527 2.2739 + 6SOL HW2 18 0.301 0.920 0.206 1.7731 -1.8814 1.6162 + 7SOL OW 19 1.513 1.574 0.936 0.3842 -0.4420 -0.5030 + 7SOL HW1 20 1.574 1.494 0.938 -0.2263 -0.8989 0.7853 + 7SOL HW2 21 1.442 1.562 1.006 -0.6014 0.5387 -1.3389 + 8SOL OW 22 1.705 1.514 1.173 -0.1702 -0.3614 -0.3611 + 8SOL HW1 23 1.787 1.568 1.154 0.2614 -1.0351 -0.4494 + 8SOL HW2 24 1.625 1.574 1.176 0.3729 0.3447 0.0718 + 9SOL OW 25 1.346 0.399 0.373 -0.2208 -0.0453 -0.6574 + 9SOL HW1 26 1.269 0.405 0.437 0.9610 0.9068 0.7214 + 9SOL HW2 27 1.330 0.324 0.309 -1.3321 -1.1942 0.9220 + 10SOL OW 28 1.416 0.982 1.612 -0.4650 -0.1622 -0.9716 + 10SOL HW1 29 1.364 0.896 1.616 0.1011 -0.4798 -0.4023 + 10SOL HW2 30 1.380 1.039 1.538 -2.3794 0.1173 0.1450 + 11SOL OW 31 0.580 1.437 1.073 -0.2634 -0.1719 -0.3125 + 11SOL HW1 32 0.642 1.501 1.117 0.1266 1.7442 -3.4466 + 11SOL HW2 33 0.587 1.447 0.974 -1.6002 -3.7856 -0.8664 + 12SOL OW 34 0.427 0.542 0.668 0.3570 0.7263 0.0563 + 12SOL HW1 35 0.376 0.513 0.587 -0.4493 2.2745 0.0104 + 12SOL HW2 36 0.375 0.611 0.719 0.8251 -0.2655 1.9426 + 13SOL OW 37 1.495 0.945 1.174 -1.1488 -0.4867 0.1959 + 13SOL HW1 38 1.551 0.866 1.152 -1.0445 -0.6151 0.9262 + 13SOL HW2 39 1.466 0.990 1.089 2.7582 1.4855 -0.2368 + 14SOL OW 40 1.416 1.196 0.728 -0.3796 -0.4794 0.0428 + 14SOL HW1 41 1.405 1.294 0.713 0.6085 -0.0873 1.8079 + 14SOL HW2 42 1.484 1.159 0.665 1.4628 0.5559 1.3969 + 15SOL OW 43 0.620 0.002 0.834 0.7178 -0.2983 -0.1199 + 15SOL HW1 44 0.575 -0.006 0.923 1.9411 0.6663 0.6031 + 15SOL HW2 45 0.570 0.067 0.777 1.3496 0.9877 0.7814 + 16SOL OW 46 1.846 0.346 0.269 -0.1832 -0.3909 0.0197 + 16SOL HW1 47 1.759 0.390 0.292 -0.9077 -1.0912 -1.3155 + 16SOL HW2 48 1.883 0.302 0.351 -1.7788 -1.2543 0.3073 + 17SOL OW 49 0.692 0.116 1.700 -0.6605 -0.4036 0.1050 + 17SOL HW1 50 0.692 0.127 1.799 -0.2191 3.9210 -0.2895 + 17SOL HW2 51 0.598 0.117 1.666 -0.7338 -0.1546 0.3150 + 18SOL OW 52 0.456 1.027 1.253 0.0478 0.5019 -0.3706 + 18SOL HW1 53 0.482 1.102 1.313 -1.2523 0.8000 -0.1722 + 18SOL HW2 54 0.374 0.981 1.288 -1.0700 1.0368 -2.1759 + 19SOL OW 55 1.527 1.387 1.709 0.4991 0.8594 0.3685 + 19SOL HW1 56 1.604 1.420 1.765 0.7981 0.5213 0.1557 + 19SOL HW2 57 1.502 1.295 1.739 -0.1853 1.1838 0.8070 + 20SOL OW 58 1.005 0.849 1.020 0.1304 -0.5491 -0.6984 + 20SOL HW1 59 0.982 0.763 1.064 -3.2011 0.9908 0.7663 + 20SOL HW2 60 0.996 0.841 0.921 0.5743 -2.0797 -0.6136 + 21SOL OW 61 0.847 0.985 0.318 -0.3275 0.1367 -0.1526 + 21SOL HW1 62 0.779 1.048 0.279 0.3971 0.1331 -1.4309 + 21SOL HW2 63 0.829 0.974 0.416 0.2348 3.2339 0.3455 + 22SOL OW 64 1.736 1.128 0.100 -0.0293 0.2335 0.2091 + 22SOL HW1 65 1.733 1.057 0.170 -0.5328 0.5273 0.4863 + 22SOL HW2 66 1.707 1.090 0.012 0.1225 -0.0120 0.2652 + 23SOL OW 67 1.674 0.501 0.732 0.2403 -0.2350 -0.5418 + 23SOL HW1 68 1.651 0.437 0.659 -0.9295 -1.0168 0.4735 + 23SOL HW2 69 1.756 0.553 0.707 1.4049 -2.3475 -1.2702 + 24SOL OW 70 1.556 1.731 1.574 0.1155 0.8419 -0.3686 + 24SOL HW1 71 1.655 1.717 1.580 -0.2880 -2.2137 -0.2410 + 24SOL HW2 72 1.514 1.654 1.526 -1.9663 3.2561 -2.6061 + 25SOL OW 73 0.253 1.336 1.345 -0.2486 -0.5643 -0.0230 + 25SOL HW1 74 0.331 1.298 1.395 0.3861 0.0393 -0.5418 + 25SOL HW2 75 0.283 1.417 1.293 -1.5380 0.5971 0.9899 + 26SOL OW 76 1.446 1.139 0.410 0.1250 0.0937 0.0640 + 26SOL HW1 77 1.392 1.177 0.335 -0.5262 -0.1962 0.3857 + 26SOL HW2 78 1.479 1.048 0.385 2.3533 1.1687 -1.0263 + 27SOL OW 79 1.225 1.804 0.578 0.0688 -0.4593 -0.5396 + 27SOL HW1 80 1.159 1.878 0.589 0.4845 -0.0547 -0.7712 + 27SOL HW2 81 1.184 1.718 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Wed Jan 3 16:28:55 2024 +Host: FAIRmat-AreaC2-Rudzinski pid: 472911 rank ID: 0 number of ranks: 1 + :-) GROMACS - gmx mdrun, 2018.6 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra + Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru + Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus + Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl + Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola + Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov + Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2017, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2018.6 +Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_ENUM_tests/integrator-md/thermostat-vrescale +Command line: + gmx mdrun -s water.tpr -o water.trr + +GROMACS version: 2018.6 +Precision: single +Memory model: 64 bit +MPI library: thread_mpi +OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) +GPU support: OpenCL +SIMD instructions: SSE2 +FFT library: fftw-3.3.8-sse2-avx +RDTSCP usage: disabled +TNG support: enabled +Hwloc support: hwloc-1.11.9 +Tracing support: disabled +Built on: 2019-05-12 20:18:02 +Built by: root@default-0e84dd72-7298-44a4-a670-e10728e370dd [CMAKE] +Build OS/arch: Linux 4.4.0-96-generic x86_64 +Build CPU vendor: Unknown +Build CPU brand: Unknown +Build CPU family: 0 Model: 0 Stepping: 0 +Build CPU features: Unknown +C compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc GNU 7.3.0 +C compiler flags: -msse2 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +C++ compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ GNU 7.3.0 +C++ compiler flags: -msse2 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +OpenCL include dir: /home/jfrudzinski/miniconda3/envs/martignac_2/include +OpenCL library: /home/jfrudzinski/miniconda3/envs/martignac_2/lib/libOpenCL.so +OpenCL version: 2.0 + +NOTE: Detection of GPUs failed. The API reported: + GROMACS cannot run tasks on a GPU. + +Running on 1 node with total 4 cores, 8 logical cores, 0 compatible GPUs +Hardware detected: + CPU info: + Vendor: Intel + Brand: 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz + Family: 6 Model: 140 Stepping: 1 + Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic + Number of AVX-512 FMA units: Cannot run AVX-512 detection - assuming 2 + Hardware topology: Full, with devices + Sockets, cores, and logical processors: + Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] + Numa nodes: + Node 0 (16138244096 bytes mem): 0 1 2 3 4 5 6 7 + Latency: + 0 + 0 1.00 + Caches: + L1: 49152 bytes, linesize 64 bytes, assoc. 12, shared 2 ways + L2: 1310720 bytes, linesize 64 bytes, assoc. 20, shared 2 ways + L3: 12582912 bytes, linesize 64 bytes, assoc. 12, shared 8 ways + PCI devices: + 0000:00:02.0 Id: 8086:9a49 Class: 0x0300 Numa: 0 + 0000:00:0e.0 Id: 8086:9a0b Class: 0x0104 Numa: 0 + 0000:00:14.3 Id: 8086:a0f0 Class: 0x0280 Numa: 0 + 0000:00:1f.6 Id: 8086:15fb Class: 0x0200 Numa: 0 + +Highest SIMD level requested by all nodes in run: AVX_512 +SIMD instructions selected at compile time: SSE2 +This program was compiled for different hardware than you are running on, +which could influence performance. + +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. +Lindahl +GROMACS: High performance molecular simulations through multi-level +parallelism from laptops to supercomputers +SoftwareX 1 (2015) pp. 19-25 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl +Tackling Exascale Software Challenges in Molecular Dynamics Simulations with +GROMACS +In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. +Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl +GROMACS 4.5: a high-throughput and highly parallel open source molecular +simulation toolkit +Bioinformatics 29 (2013) pp. 845-54 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl +GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable +molecular simulation +J. Chem. Theory Comput. 4 (2008) pp. 435-447 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. +Berendsen +GROMACS: Fast, Flexible and Free +J. Comp. Chem. 26 (2005) pp. 1701-1719 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +E. Lindahl and B. Hess and D. van der Spoel +GROMACS 3.0: A package for molecular simulation and trajectory analysis +J. Mol. Mod. 7 (2001) pp. 306-317 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +H. J. C. Berendsen, D. van der Spoel and R. van Drunen +GROMACS: A message-passing parallel molecular dynamics implementation +Comp. Phys. Comm. 91 (1995) pp. 43-56 +-------- -------- --- Thank You --- -------- -------- + +Input Parameters: + integrator = md + tinit = 0 + dt = 0.001 + nsteps = 1 + init-step = 0 + simulation-part = 1 + comm-mode = Linear + nstcomm = 1 + bd-fric = 0 + ld-seed = -1278295868 + emtol = 10 + emstep = 0.01 + niter = 20 + fcstep = 0 + nstcgsteep = 1000 + nbfgscorr = 10 + rtpi = 0.05 + nstxout = 1 + nstvout = 1 + nstfout = 1 + nstlog = 1 + nstcalcenergy = 1 + nstenergy = 1 + nstxout-compressed = 0 + compressed-x-precision = 1000 + cutoff-scheme = Verlet + nstlist = 1 + ns-type = Grid + pbc = xyz + periodic-molecules = false + verlet-buffer-tolerance = 0.005 + rlist = 0.9 + coulombtype = PME + coulomb-modifier = Potential-shift + rcoulomb-switch = 0 + rcoulomb = 0.9 + epsilon-r = 1 + epsilon-rf = inf + vdw-type = Cut-off + vdw-modifier = Potential-shift + rvdw-switch = 0 + rvdw = 0.9 + DispCorr = EnerPres + table-extension = 1 + fourierspacing = 0.08 + fourier-nx = 24 + fourier-ny = 24 + fourier-nz = 24 + pme-order = 6 + ewald-rtol = 1e-06 + ewald-rtol-lj = 0.001 + lj-pme-comb-rule = Geometric + ewald-geometry = 0 + epsilon-surface = 0 + implicit-solvent = No + gb-algorithm = Still + nstgbradii = 1 + rgbradii = 1 + gb-epsilon-solvent = 80 + gb-saltconc = 0 + gb-obc-alpha = 1 + gb-obc-beta = 0.8 + gb-obc-gamma = 4.85 + gb-dielectric-offset = 0.009 + sa-algorithm = Ace-approximation + sa-surface-tension = 2.05016 + tcoupl = V-rescale + nsttcouple = 1 + nh-chain-length = 0 + print-nose-hoover-chain-variables = false + pcoupl = No + pcoupltype = Isotropic + nstpcouple = -1 + tau-p = 5 + compressibility (3x3): + compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p (3x3): + ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + refcoord-scaling = No + posres-com (3): + posres-com[0]= 0.00000e+00 + posres-com[1]= 0.00000e+00 + posres-com[2]= 0.00000e+00 + posres-comB (3): + posres-comB[0]= 0.00000e+00 + posres-comB[1]= 0.00000e+00 + posres-comB[2]= 0.00000e+00 + QMMM = false + QMconstraints = 0 + QMMMscheme = 0 + MMChargeScaleFactor = 1 +qm-opts: + ngQM = 0 + constraint-algorithm = Lincs + continuation = false + Shake-SOR = false + shake-tol = 0.0001 + lincs-order = 4 + lincs-iter = 1 + lincs-warnangle = 30 + nwall = 0 + wall-type = 9-3 + wall-r-linpot = -1 + wall-atomtype[0] = -1 + wall-atomtype[1] = -1 + wall-density[0] = 0 + wall-density[1] = 0 + wall-ewald-zfac = 3 + pull = false + awh = false + rotation = false + interactiveMD = false + disre = No + disre-weighting = Conservative + disre-mixed = false + dr-fc = 1000 + dr-tau = 0 + nstdisreout = 100 + orire-fc = 0 + orire-tau = 0 + nstorireout = 100 + free-energy = no + cos-acceleration = 0 + deform (3x3): + deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + simulated-tempering = false + swapcoords = no + userint1 = 0 + userint2 = 0 + userint3 = 0 + userint4 = 0 + userreal1 = 0 + userreal2 = 0 + userreal3 = 0 + userreal4 = 0 + applied-forces: + electric-field: + x: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + y: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + z: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 +grpopts: + nrdf: 1293 + ref-t: 298 + tau-t: 0.5 +annealing: No +annealing-npoints: 0 + acc: 0 0 0 + nfreeze: N N N + energygrp-flags[ 0]: 0 + + +Using 1 MPI thread +Using 8 OpenMP threads + +Pinning threads with an auto-selected logical core stride of 1 +System total charge: 0.000 +Will do PME sum in reciprocal space for electrostatic interactions. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen +A smooth particle mesh Ewald method +J. Chem. Phys. 103 (1995) pp. 8577-8592 +-------- -------- --- Thank You --- -------- -------- + +Using a Gaussian width (1/beta) of 0.260197 nm for Ewald +Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-06 +Initialized non-bonded Ewald correction tables, spacing: 8.41e-04 size: 1071 + +Long Range LJ corr.: 2.9078e-04 +Generated table with 950 data points for Ewald. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ6. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ12. +Tabscale = 500 points/nm + +Using SIMD 4x4 nonbonded short-range kernels + +Using a 4x4 pair-list setup: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm +At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm + +Using geometric Lennard-Jones combination rule + +Removing pbc first time + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Miyamoto and P. A. Kollman +SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid +Water Models +J. Comp. Chem. 13 (1992) pp. 952-962 +-------- -------- --- Thank You --- -------- -------- + + +Intra-simulation communication will occur every 1 steps. +Center of mass motion removal mode is Linear +We have the following groups for center of mass motion removal: + 0: rest + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +G. Bussi, D. Donadio and M. Parrinello +Canonical sampling through velocity rescaling +J. Chem. Phys. 126 (2007) pp. 014101 +-------- -------- --- Thank You --- -------- -------- + +There are: 648 Atoms + +Constraining the starting coordinates (step 0) + +Constraining the coordinates at t0-dt (step 0) +RMS relative constraint deviation after constraining: 0.00e+00 +Initial temperature: 303.778 K + +Started mdrun on rank 0 Wed Jan 3 16:28:56 2024 + Step Time + 0 0.00000 + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.98181e+03 -1.08747e+02 -1.21912e+04 1.28385e+02 -1.01898e+04 + Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) + 1.63107e+03 -8.55869e+03 -8.55632e+03 3.03438e+02 -2.80811e+02 + Pressure (bar) + -4.80332e+02 + + Step Time + 1 0.00100 + +Writing checkpoint, step 1 at Wed Jan 3 16:28:56 2024 + + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97589e+03 -1.08747e+02 -1.21828e+04 1.28144e+02 -1.01875e+04 + Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) + 1.62706e+03 -8.56049e+03 -8.55690e+03 3.02691e+02 -2.80811e+02 + Pressure (bar) + -5.27071e+02 + + <====== ############### ==> + <==== A V E R A G E S ====> + <== ############### ======> + + Statistics over 2 steps using 2 frames + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97885e+03 -1.08747e+02 -1.21870e+04 1.28265e+02 -1.01887e+04 + Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) + 1.62906e+03 -8.55959e+03 -8.55661e+03 3.03065e+02 -2.80811e+02 + Pressure (bar) + -5.03701e+02 + + Total Virial (kJ/mol) + 6.68027e+02 1.09404e+02 1.76408e+02 + 1.09855e+02 5.40926e+02 -2.23449e+01 + 1.76941e+02 -2.25064e+01 7.13182e+02 + + Pressure (bar) + -8.03212e+02 -4.57444e+02 -9.62101e+02 + -4.59767e+02 2.19365e+02 6.04812e+01 + -9.64854e+02 6.13141e+01 -9.27258e+02 + + + M E G A - F L O P S A C C O U N T I N G + + NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels + RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table + W3=SPC/TIP3p W4=TIP4p (single or pairs) + V&F=Potential and force V=Potential only F=Force only + + Computing: M-Number M-Flops % Flops +----------------------------------------------------------------------------- + Pair Search distance check 0.306406 2.758 8.6 + NxN QSTab Elec. + LJ [V&F] 0.207760 12.258 38.2 + NxN QSTab Elec. [V&F] 0.198560 8.141 25.3 + Calc Weights 0.003888 0.140 0.4 + Spread Q Bspline 0.279936 0.560 1.7 + Gather F Bspline 0.279936 1.680 5.2 + 3D-FFT 0.760588 6.085 18.9 + Solve PME 0.001152 0.074 0.2 + Shift-X 0.001296 0.008 0.0 + Virial 0.001386 0.025 0.1 + Stop-CM 0.001944 0.019 0.1 + Calc-Ekin 0.001944 0.052 0.2 + Constraint-V 0.001944 0.016 0.0 + Constraint-Vir 0.001296 0.031 0.1 + Settle 0.000864 0.279 0.9 +----------------------------------------------------------------------------- + Total 32.125 100.0 +----------------------------------------------------------------------------- + + + R E A L C Y C L E A N D T I M E A C C O U N T I N G + +On 1 MPI rank, each using 8 OpenMP threads + + Computing: Num Num Call Wall time Giga-Cycles + Ranks Threads Count (s) total sum % +----------------------------------------------------------------------------- + Neighbor search 1 8 2 0.001 0.012 3.4 + Force 1 8 2 0.000 0.005 1.3 + PME mesh 1 8 2 0.000 0.005 1.5 + NB X/F buffer ops. 1 8 2 0.000 0.000 0.0 + Write traj. 1 8 2 0.015 0.214 61.9 + Update 1 8 2 0.006 0.090 26.0 + Constraints 1 8 2 0.000 0.000 0.1 + Rest 0.001 0.020 5.8 +----------------------------------------------------------------------------- + Total 0.024 0.345 100.0 +----------------------------------------------------------------------------- + Breakdown of PME mesh computation +----------------------------------------------------------------------------- + PME spread 1 8 2 0.000 0.002 0.6 + PME gather 1 8 2 0.000 0.002 0.4 + PME 3D-FFT 1 8 4 0.000 0.001 0.4 + PME solve Elec 1 8 2 0.000 0.000 0.1 +----------------------------------------------------------------------------- + + Core t (s) Wall t (s) (%) + Time: 0.191 0.024 800.0 + (ns/day) (hour/ns) +Performance: 7.236 3.317 +Finished mdrun on rank 0 Wed Jan 3 16:28:56 2024 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/mdout.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/mdout.mdp new file mode 100644 index 00000000..e3830c1a --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/mdout.mdp @@ -0,0 +1,353 @@ +; +; File 'mdout.mdp' was generated +; By user: jfrudzinski (1000) +; On host: FAIRmat-AreaC2-Rudzinski +; At date: Wed Jan 3 16:28:55 2024 +; +; Created by: +; :-) GROMACS - gmx grompp, 2018.6 (-: +; +; Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +; Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +; Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_ENUM_tests/integrator-md/thermostat-vrescale +; Command line: +; gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +; VARIOUS PREPROCESSING OPTIONS +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/roe +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ +; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) +define = + +; RUN CONTROL PARAMETERS +integrator = md +; Start time and timestep in ps +tinit = 0.0 +dt = 0.001 +nsteps = 1 +; For exact run continuation or redoing part of a run +init-step = 0 +; Part index is updated automatically on checkpointing (keeps files separate) +simulation-part = 1 +; mode for center of mass motion removal +comm-mode = linear +; number of steps for center of mass motion removal +nstcomm = 1 +; group(s) for center of mass motion removal +comm-grps = + +; LANGEVIN DYNAMICS OPTIONS +; Friction coefficient (amu/ps) and random seed +bd-fric = 0 +ld-seed = -1 + +; ENERGY MINIMIZATION OPTIONS +; Force tolerance and initial step-size +emtol = 10 +emstep = 0.01 +; Max number of iterations in relax-shells +niter = 20 +; Step size (ps^2) for minimization of flexible constraints +fcstep = 0 +; Frequency of steepest descents steps when doing CG +nstcgsteep = 1000 +nbfgscorr = 10 + +; TEST PARTICLE INSERTION OPTIONS +rtpi = 0.05 + +; OUTPUT CONTROL OPTIONS +; Output frequency for coords (x), velocities (v) and forces (f) +nstxout = 1 +nstvout = 1 +nstfout = 1 +; Output frequency for energies to log file and energy file +nstlog = 1 +nstcalcenergy = 100 +nstenergy = 1 +; Output frequency and precision for .xtc file +nstxout-compressed = 0 +compressed-x-precision = 1000 +; This selects the subset of atoms for the compressed +; trajectory file. You can select multiple groups. By +; default, all atoms will be written. +compressed-x-grps = +; Selection of energy groups +energygrps = System + +; NEIGHBORSEARCHING PARAMETERS +; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) +cutoff-scheme = Verlet +; nblist update frequency +nstlist = 1 +; ns algorithm (simple or grid) +ns_type = grid +; Periodic boundary conditions: xyz, no, xy +pbc = xyz +periodic-molecules = no +; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, +; a value of -1 means: use rlist +verlet-buffer-tolerance = 0.005 +; nblist cut-off +rlist = 0.9 +; long-range cut-off for switched potentials + +; OPTIONS FOR ELECTROSTATICS AND VDW +; Method for doing electrostatics +coulombtype = PME +coulomb-modifier = Potential-shift-Verlet +rcoulomb-switch = 0 +rcoulomb = 0.9 +; Relative dielectric constant for the medium and the reaction field +epsilon-r = 1 +epsilon-rf = 0 +; Method for doing Van der Waals +vdwtype = cutoff +vdw-modifier = Potential-shift-Verlet +; cut-off lengths +rvdw-switch = 0 +rvdw = 0.9 +; Apply long range dispersion corrections for Energy and Pressure +DispCorr = EnerPres +; Extension of the potential lookup tables beyond the cut-off +table-extension = 1 +; Separate tables between energy group pairs +energygrp-table = +; Spacing for the PME/PPPM FFT grid +fourierspacing = 0.08 +; FFT grid size, when a value is 0 fourierspacing will be used +fourier-nx = 0 +fourier-ny = 0 +fourier-nz = 0 +; EWALD/PME/PPPM parameters +pme_order = 6 +ewald_rtol = 1e-06 +ewald-rtol-lj = 0.001 +lj-pme-comb-rule = Geometric +ewald-geometry = 3d +epsilon-surface = 0 + +; IMPLICIT SOLVENT ALGORITHM +implicit-solvent = No + +; GENERALIZED BORN ELECTROSTATICS +; Algorithm for calculating Born radii +gb-algorithm = Still +; Frequency of calculating the Born radii inside rlist +nstgbradii = 1 +; Cutoff for Born radii calculation; the contribution from atoms +; between rlist and rgbradii is updated every nstlist steps +rgbradii = 1 +; Dielectric coefficient of the implicit solvent +gb-epsilon-solvent = 80 +; Salt concentration in M for Generalized Born models +gb-saltconc = 0 +; Scaling factors used in the OBC GB model. Default values are OBC(II) +gb-obc-alpha = 1 +gb-obc-beta = 0.8 +gb-obc-gamma = 4.85 +gb-dielectric-offset = 0.009 +sa-algorithm = Ace-approximation +; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA +; The value -1 will set default value for Still/HCT/OBC GB-models. +sa-surface-tension = -1 + +; OPTIONS FOR WEAK COUPLING ALGORITHMS +; Temperature coupling +tcoupl = v-rescale +nsttcouple = -1 +nh-chain-length = 10 +print-nose-hoover-chain-variables = no +; Groups to couple separately +tc_grps = System +; Time constant (ps) and reference temperature (K) +tau_t = 0.5 +ref_t = 298 +; pressure coupling +pcoupl = no +pcoupltype = Isotropic +nstpcouple = -1 +; Time constant (ps), compressibility (1/bar) and reference P (bar) +tau-p = 5.0 +compressibility = 7.4e-5 +ref-p = 1.0 +; Scaling of reference coordinates, No, All or COM +refcoord-scaling = No + +; OPTIONS FOR QMMM calculations +QMMM = no +; Groups treated Quantum Mechanically +QMMM-grps = +; QM method +QMmethod = +; QMMM scheme +QMMMscheme = normal +; QM basisset +QMbasis = +; QM charge +QMcharge = +; QM multiplicity +QMmult = +; Surface Hopping +SH = +; CAS space options +CASorbitals = +CASelectrons = +SAon = +SAoff = +SAsteps = +; Scale factor for MM charges +MMChargeScaleFactor = 1 + +; SIMULATED ANNEALING +; Type of annealing for each temperature group (no/single/periodic) +annealing = +; Number of time points to use for specifying annealing in each group +annealing-npoints = +; List of times at the annealing points for each group +annealing-time = +; Temp. at each annealing point, for each group. +annealing-temp = + +; GENERATE VELOCITIES FOR STARTUP RUN +gen-vel = no +gen-temp = 300 +gen-seed = -1 + +; OPTIONS FOR BONDS +constraints = none +; Type of constraint algorithm +constraint-algorithm = Lincs +; Do not constrain the start configuration +continuation = no +; Use successive overrelaxation to reduce the number of shake iterations +Shake-SOR = no +; Relative tolerance of shake +shake-tol = 0.0001 +; Highest order in the expansion of the constraint coupling matrix +lincs-order = 4 +; Number of iterations in the final step of LINCS. 1 is fine for +; normal simulations, but use 2 to conserve energy in NVE runs. +; For energy minimization with constraints it should be 4 to 8. +lincs-iter = 1 +; Lincs will write a warning to the stderr if in one step a bond +; rotates over more degrees than +lincs-warnangle = 30 +; Convert harmonic bonds to morse potentials +morse = no + +; ENERGY GROUP EXCLUSIONS +; Pairs of energy groups for which all non-bonded interactions are excluded +energygrp-excl = + +; WALLS +; Number of walls, type, atom types, densities and box-z scale factor for Ewald +nwall = 0 +wall-type = 9-3 +wall-r-linpot = -1 +wall-atomtype = +wall-density = +wall-ewald-zfac = 3 + +; COM PULLING +pull = no + +; AWH biasing +awh = no + +; ENFORCED ROTATION +; Enforced rotation: No or Yes +rotation = no + +; Group to display and/or manipulate in interactive MD session +IMD-group = + +; NMR refinement stuff +; Distance restraints type: No, Simple or Ensemble +disre = No +; Force weighting of pairs in one distance restraint: Conservative or Equal +disre-weighting = Conservative +; Use sqrt of the time averaged times the instantaneous violation +disre-mixed = no +disre-fc = 1000 +disre-tau = 0 +; Output frequency for pair distances to energy file +nstdisreout = 100 +; Orientation restraints: No or Yes +orire = no +; Orientation restraints force constant and tau for time averaging +orire-fc = 0 +orire-tau = 0 +orire-fitgrp = +; Output frequency for trace(SD) and S to energy file +nstorireout = 100 + +; Free energy variables +free-energy = no +couple-moltype = +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q +couple-intramol = no +init-lambda = -1 +init-lambda-state = -1 +delta-lambda = 0 +nstdhdl = 50 +fep-lambdas = +mass-lambdas = +coul-lambdas = +vdw-lambdas = +bonded-lambdas = +restraint-lambdas = +temperature-lambdas = +calc-lambda-neighbors = 1 +init-lambda-weights = +dhdl-print-energy = no +sc-alpha = 0 +sc-power = 1 +sc-r-power = 6 +sc-sigma = 0.3 +sc-coul = no +separate-dhdl-file = yes +dhdl-derivatives = yes +dh_hist_size = 0 +dh_hist_spacing = 0.1 + +; Non-equilibrium MD stuff +acc-grps = +accelerate = +freezegrps = +freezedim = +cos-acceleration = 0 +deform = + +; simulated tempering variables +simulated-tempering = no +simulated-tempering-scaling = geometric +sim-temp-low = 300 +sim-temp-high = 300 + +; Ion/water position swapping for computational electrophysiology setups +; Swap positions along direction: no, X, Y, Z +swapcoords = no +adress = no + +; User defined thingies +user1-grps = +user2-grps = +userint1 = 0 +userint2 = 0 +userint3 = 0 +userint4 = 0 +userreal1 = 0 +userreal2 = 0 +userreal3 = 0 +userreal4 = 0 +; Electric fields +; Format for electric-field-x, etc. is: four real variables: +; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), +; and sigma (ps) width of the pulse. Omega = 0 means static field, +; sigma = 0 means no pulse, leaving the field to be a cosine function. +electric-field-x = 0 0 0 0 +electric-field-y = 0 0 0 0 +electric-field-z = 0 0 0 0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/state.cpt b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/state.cpt new file mode 100644 index 00000000..f4f8a07b Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/state.cpt differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.298.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.298.mdp new file mode 100644 index 00000000..b410d318 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.298.mdp @@ -0,0 +1,52 @@ +; Preprocessing +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ + +; Run Control +integrator = md +tinit = 0.0 +dt = 0.001 ; 1.0 fs +nsteps = 1 ; 20 ns +nstcomm = 1 ; no. steps between removing com motion +comm-mode = linear ; remove com translation + +; Output Control +nstxout = 1 ; no. steps between printing coords to trr file => 1ps +nstvout = 1 ; no. steps between printing veloc to trr file +nstfout = 1 ; no. steps between printing forces to trr file => 1ps +nstlog = 1 ; no. steps between printing energy to log file => 1ps +nstenergy = 1 ; no. steps between printing energy to edr file => 1ps +nstxtcout = 0 ; no. stpes between printing coords to xtc file +energygrps = System ; groups for writing energy file + +; Neighbor searching +nstlist = 1 ; update neighbor list every step +ns_type = grid ; check neighbor list using grid +rlist = 0.9 ; cutoff distance (nm) for short-range neighbor list + +; Electrostatics and VdW +coulombtype = PME ; fast particle-mesh ewald electrostatics +rcoulomb = 0.9 ; distance for the Coulomb cut-off +vdwtype = cutoff ; truncated LJ interactions +rvdw = 0.9 ; distance for LJ cut-off +DispCorr = EnerPres ; apply long range disp. correct. for Energy/Pres +fourierspacing = 0.08 ; max grid spacing fr FFT grid in PME +pme_order = 6 ; interpolation order for PME +ewald_rtol = 1e-06 ; relative strength of direct potential at cutoff +optimize_fft = yes ; optimize fft_grids + +; Temperature Coupling +tcoupl = v-rescale ; nose-hoover for correct ensemble +tc_grps = System ; groups to couple separtly to temp. bath +tau_t = 0.5 ; time constant for coupling +ref_t = 298 ; ref. temperature for coupling + +; Velocity generation +;gen_vel = yes ; generate velocities with Max. dist. +;gen_temp = 298 ; temp. for Max. dist. +;gen_seed = 173529 ; for random number generator + +; Pressure coupling +pcoupl = no +tau-p = 5.0 +compressibility = 7.4e-5 +ref-p = 1.0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.confout.gro new file mode 100644 index 00000000..0244d504 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.427 0.087 1.634 0.0670 0.6261 -0.3260 + 1SOL HW1 2 0.352 0.153 1.636 -0.6525 -0.2083 0.2628 + 1SOL HW2 3 0.394 -0.001 1.600 1.0005 0.5272 -1.0056 + 2SOL OW 4 0.365 0.990 0.648 0.2321 -0.9063 -0.2980 + 2SOL HW1 5 0.377 0.914 0.584 -0.7093 -1.6057 0.3416 + 2SOL HW2 6 0.274 1.030 0.635 -0.0303 -1.1620 0.7020 + 3SOL OW 7 1.293 1.628 1.682 0.0780 0.2611 -0.6033 + 3SOL HW1 8 1.334 1.698 1.741 0.7308 -0.2019 -0.4969 + 3SOL HW2 9 1.365 1.565 1.651 -0.3690 0.1198 -1.3618 + 4SOL OW 10 0.922 1.027 1.587 -0.3854 -0.0836 0.3470 + 4SOL HW1 11 0.948 1.121 1.565 0.9210 -0.3821 0.5298 + 4SOL HW2 12 0.938 1.009 1.684 -0.7039 -0.4697 0.3326 + 5SOL OW 13 0.871 1.326 0.395 -0.6365 0.2971 0.0566 + 5SOL HW1 14 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HW2 492 0.759 0.951 1.294 0.9741 -0.4442 -1.7936 + 165SOL OW 493 1.401 1.470 0.695 -0.2650 -0.1147 -0.2591 + 165SOL HW1 494 1.448 1.512 0.773 0.1362 -1.3127 0.1498 + 165SOL HW2 495 1.314 1.516 0.681 0.1335 0.8152 0.2286 + 166SOL OW 496 1.689 0.901 0.642 0.6285 -0.6176 0.3168 + 166SOL HW1 497 1.595 0.867 0.646 -0.0387 1.2285 1.2251 + 166SOL HW2 498 1.750 0.837 0.688 -0.2796 -1.5063 0.3089 + 167SOL OW 499 0.628 0.054 1.130 0.2658 0.5578 0.4262 + 167SOL HW1 500 0.567 0.118 1.083 0.9225 1.0149 0.1985 + 167SOL HW2 501 0.619 0.067 1.228 0.5776 1.1660 0.3761 + 168SOL OW 502 1.284 0.547 0.943 -0.1774 -0.2154 -0.0182 + 168SOL HW1 503 1.228 0.494 1.007 -1.2285 1.6389 0.6648 + 168SOL HW2 504 1.362 0.586 0.993 -0.9588 1.1735 0.1511 + 169SOL OW 505 0.830 0.328 0.586 0.4046 -0.2408 0.4182 + 169SOL HW1 506 0.814 0.426 0.572 1.0997 0.0252 1.4337 + 169SOL HW2 507 0.793 0.300 0.674 0.2024 -0.9005 0.1273 + 170SOL OW 508 1.831 1.624 0.059 0.3766 0.4513 -0.0063 + 170SOL HW1 509 1.926 1.599 0.041 -0.2526 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176SOL HW1 527 1.752 1.801 0.651 0.1077 -0.5009 0.1463 + 176SOL HW2 528 1.795 1.698 0.532 -1.7189 0.6857 -1.5890 + 177SOL OW 529 0.801 1.384 1.478 -0.5577 0.3550 -0.3805 + 177SOL HW1 530 0.727 1.443 1.509 0.3489 1.3029 0.0091 + 177SOL HW2 531 0.873 1.381 1.548 -0.6467 -1.3305 -0.3211 + 178SOL OW 532 0.703 0.578 0.619 0.2456 -0.5121 -0.0258 + 178SOL HW1 533 0.706 0.644 0.544 0.1046 0.1791 0.5645 + 178SOL HW2 534 0.609 0.546 0.632 0.2652 -0.6092 -0.1228 + 179SOL OW 535 1.069 1.528 1.490 -0.4791 0.3219 0.1074 + 179SOL HW1 536 1.089 1.431 1.506 1.6026 0.3421 -2.1362 + 179SOL HW2 537 1.153 1.581 1.492 -1.3336 1.7645 -0.8926 + 180SOL OW 538 0.331 1.507 0.882 0.0830 0.6824 0.3473 + 180SOL HW1 539 0.351 1.445 0.958 0.4365 0.0094 -0.2907 + 180SOL HW2 540 0.235 1.499 0.857 0.6896 -1.4571 -1.3748 + 181SOL OW 541 1.370 0.007 0.942 0.3182 -0.3568 -0.3435 + 181SOL HW1 542 1.432 -0.071 0.940 0.0645 -0.5854 0.5377 + 181SOL HW2 543 1.282 -0.018 0.902 -0.8327 -1.4792 2.7400 + 182SOL OW 544 0.253 0.428 0.457 -0.0183 0.3143 0.3329 + 182SOL HW1 545 0.311 0.351 0.430 -0.1553 1.1020 -2.4236 + 182SOL HW2 546 0.170 0.393 0.502 1.6909 -0.9043 2.6201 + 183SOL OW 547 0.286 0.097 1.177 0.5078 -0.0262 -0.1346 + 183SOL HW1 548 0.219 0.171 1.184 -0.0027 -0.3660 -1.2136 + 183SOL HW2 549 0.367 0.130 1.128 1.1385 0.3882 1.1809 + 184SOL OW 550 0.025 1.844 1.398 0.8241 0.0883 -0.4432 + 184SOL HW1 551 0.099 1.895 1.442 1.8365 -1.9952 0.2967 + 184SOL HW2 552 -0.012 1.776 1.461 -0.4736 -0.1561 -1.4373 + 185SOL OW 553 0.534 0.658 1.575 -0.3340 0.3639 -0.0368 + 185SOL HW1 554 0.574 0.664 1.667 0.3355 -1.0454 -0.2294 + 185SOL HW2 555 0.607 0.657 1.507 -0.6335 -2.9360 -0.3589 + 186SOL OW 556 1.418 0.775 0.820 -0.0169 1.0421 -0.8445 + 186SOL HW1 557 1.378 0.691 0.857 0.7531 1.3106 0.6462 + 186SOL HW2 558 1.398 0.782 0.723 -0.6095 -0.5640 -0.8452 + 187SOL OW 559 0.222 0.944 1.345 -0.2158 0.3297 -0.7016 + 187SOL HW1 560 0.131 0.904 1.335 -0.6758 0.9556 0.9203 + 187SOL HW2 561 0.226 0.999 1.428 1.2918 1.2851 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1.374 0.7114 0.8100 1.8430 + 194SOL OW 580 1.424 1.837 1.808 0.0919 -0.5746 -0.2857 + 194SOL HW1 581 1.486 1.823 1.731 0.4877 1.9227 -0.4851 + 194SOL HW2 582 1.478 1.861 1.889 -0.4948 0.0238 -0.0653 + 195SOL OW 583 0.658 1.239 0.620 -0.3609 0.5478 -0.5495 + 195SOL HW1 584 0.747 1.197 0.604 -0.5919 0.8796 -2.7776 + 195SOL HW2 585 0.604 1.180 0.680 0.7884 -0.3959 -0.4194 + 196SOL OW 586 1.379 0.250 1.783 0.0082 -0.7042 0.3366 + 196SOL HW1 587 1.419 0.159 1.771 2.8172 0.8867 -3.3603 + 196SOL HW2 588 1.436 0.303 1.846 -0.5107 -0.8573 0.9364 + 197SOL OW 589 1.406 0.936 0.182 0.4528 -0.1813 0.0754 + 197SOL HW1 590 1.402 0.861 0.116 0.2006 -1.4207 1.4793 + 197SOL HW2 591 1.314 0.957 0.216 0.8623 -1.2400 1.8888 + 198SOL OW 592 0.030 0.412 1.436 0.2007 -0.0565 -0.4994 + 198SOL HW1 593 0.098 0.476 1.400 -0.3590 1.3329 0.8709 + 198SOL HW2 594 -0.018 0.453 1.513 -1.5666 -1.3714 -0.8498 + 199SOL OW 595 0.013 1.493 0.579 -0.5266 -0.7272 0.0410 + 199SOL HW1 596 0.039 1.479 0.675 -1.1788 1.6396 0.5768 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1.566 -0.0595 0.0259 0.7478 + 205SOL HW2 615 1.830 1.176 1.427 -1.0958 0.2748 0.4670 + 206SOL OW 616 1.671 1.161 0.622 0.0381 -0.1968 -0.8982 + 206SOL HW1 617 1.659 1.062 0.624 1.0081 -0.2945 0.2200 + 206SOL HW2 618 1.665 1.194 0.528 -3.4793 -0.9138 -0.9865 + 207SOL OW 619 0.744 0.684 1.371 -0.4972 -0.4176 0.1462 + 207SOL HW1 620 0.819 0.647 1.316 -0.8700 -0.5741 -0.2655 + 207SOL HW2 621 0.664 0.697 1.313 -0.0811 1.9892 0.0593 + 208SOL OW 622 0.821 0.317 1.194 0.4536 0.4539 -0.3308 + 208SOL HW1 623 0.766 0.361 1.123 1.4276 0.6847 -0.9606 + 208SOL HW2 624 0.768 0.311 1.279 -0.1401 1.6828 -0.6050 + 209SOL OW 625 1.664 1.037 1.689 -0.3971 0.4743 0.3950 + 209SOL HW1 626 1.571 1.024 1.655 -0.4077 -0.2767 0.7076 + 209SOL HW2 627 1.711 1.105 1.632 -0.9022 0.3384 -0.1894 + 210SOL OW 628 1.819 0.231 0.807 -0.1924 0.5243 -0.1692 + 210SOL HW1 629 1.852 0.144 0.844 1.0633 0.7808 -0.6607 + 210SOL HW2 630 1.720 0.239 0.823 0.0839 0.0674 2.0047 + 211SOL OW 631 0.979 1.242 0.144 -0.2018 0.2018 -0.0354 + 211SOL HW1 632 0.938 1.316 0.090 -0.6232 -0.6929 -0.9633 + 211SOL HW2 633 0.946 1.247 0.238 -0.1197 1.2714 -0.0561 + 212SOL OW 634 0.778 0.948 0.748 0.5845 0.0149 -0.7815 + 212SOL HW1 635 0.818 1.006 0.676 -0.1841 1.1423 -0.3163 + 212SOL HW2 636 0.695 0.991 0.783 1.4375 -0.0808 1.4255 + 213SOL OW 637 1.814 1.673 1.613 -0.0991 0.5855 0.0909 + 213SOL HW1 638 1.826 1.683 1.712 0.1001 -0.7483 0.2122 + 213SOL HW2 639 1.873 1.599 1.580 -0.2204 0.9765 -1.0148 + 214SOL OW 640 0.068 1.175 1.260 0.2612 0.5460 0.5693 + 214SOL HW1 641 0.147 1.235 1.273 0.1725 0.8319 -0.1693 + 214SOL HW2 642 0.100 1.081 1.245 0.4518 0.6382 0.3995 + 215SOL OW 643 1.089 0.245 0.891 -0.1119 0.5785 0.4751 + 215SOL HW1 644 0.994 0.267 0.866 -0.3021 -0.0338 0.6459 + 215SOL HW2 645 1.099 0.146 0.898 0.6144 0.6299 0.1871 + 216SOL OW 646 1.135 1.550 0.658 0.1441 0.6409 -0.1721 + 216SOL HW1 647 1.078 1.522 0.736 0.3615 1.9482 0.4795 + 216SOL HW2 648 1.131 1.480 0.587 0.5499 -0.9515 1.3195 + 1.86060 1.86060 1.86060 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.top b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.top new file mode 100644 index 00000000..132cf50f --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.top @@ -0,0 +1,16 @@ +; +; +; Topology file for spce water +; +; +; +#include "oplsaa.ff/forcefield.itp" + +#include "oplsaa.ff/spce.itp" + +[ system ] +spce water + +[ molecules ] +SOL 216 + diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.tpr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.tpr new file mode 100644 index 00000000..e839739e Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.tpr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.trr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.trr new file mode 100644 index 00000000..e5fe40be Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/water.trr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/commands.sh b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/commands.sh new file mode 100755 index 00000000..2e31bc08 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/commands.sh @@ -0,0 +1,3 @@ +gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +gmx mdrun -s water.tpr -o water.trr diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/confout.gro new file mode 100644 index 00000000..1d195049 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.427 0.087 1.634 0.0502 0.4642 -0.4468 + 1SOL HW1 2 0.353 0.154 1.635 0.8071 1.3228 -1.3076 + 1SOL HW2 3 0.393 0.000 1.598 -0.1660 1.2868 -2.2333 + 2SOL OW 4 0.366 0.991 0.648 0.5694 0.5339 -0.2542 + 2SOL HW1 5 0.377 0.913 0.585 -0.3811 -0.6344 1.0139 + 2SOL HW2 6 0.275 1.030 0.635 0.4199 0.3674 0.3089 + 3SOL OW 7 1.293 1.628 1.682 0.0274 0.3141 -0.2595 + 3SOL HW1 8 1.334 1.697 1.742 0.0850 -0.6462 0.8091 + 3SOL HW2 9 1.364 1.565 1.650 -0.1838 0.1924 -0.4953 + 4SOL OW 10 0.922 1.027 1.588 -0.0718 0.0237 0.6865 + 4SOL HW1 11 0.948 1.121 1.567 -0.4194 0.2800 1.4208 + 4SOL HW2 12 0.939 1.008 1.684 1.0000 -0.9924 0.3011 + 5SOL OW 13 0.871 1.326 0.395 -0.0798 0.0064 -0.2297 + 5SOL HW1 14 0.954 1.367 0.432 -0.0945 -0.2519 0.0842 + 5SOL HW2 15 0.792 1.381 0.422 -0.1617 -0.5910 0.7183 + 6SOL OW 16 0.300 0.863 0.124 -0.1946 -0.4115 -0.1384 + 6SOL HW1 17 0.252 0.910 0.050 0.1152 1.7747 1.0641 + 6SOL HW2 18 0.299 0.920 0.206 0.0971 -2.5294 1.3318 + 7SOL OW 19 1.514 1.574 0.937 0.7393 0.0901 0.1311 + 7SOL HW1 20 1.575 1.495 0.938 0.6238 0.0059 0.7537 + 7SOL HW2 21 1.442 1.562 1.006 -0.4250 -0.1557 -1.1129 + 8SOL OW 22 1.705 1.514 1.173 -0.2883 -0.1620 -0.3586 + 8SOL HW1 23 1.787 1.568 1.156 0.7266 -1.1234 1.5680 + 8SOL HW2 24 1.625 1.574 1.176 0.5993 0.9963 -0.1921 + 9SOL OW 25 1.346 0.399 0.374 -0.2308 0.3575 -0.3200 + 9SOL HW1 26 1.268 0.404 0.436 0.3427 -0.8511 0.4742 + 9SOL HW2 27 1.332 0.324 0.309 0.9855 -0.7834 0.7573 + 10SOL OW 28 1.416 0.982 1.613 -0.0835 0.3559 -0.2084 + 10SOL HW1 29 1.364 0.897 1.616 0.0088 0.2727 -0.9252 + 10SOL HW2 30 1.381 1.040 1.539 -0.6054 1.2399 0.7248 + 11SOL OW 31 0.580 1.437 1.073 -0.4847 -0.0644 -0.1413 + 11SOL HW1 32 0.643 1.498 1.120 0.4537 -0.8068 -0.4277 + 11SOL HW2 33 0.587 1.451 0.974 -0.9736 0.0518 -0.1619 + 12SOL OW 34 0.427 0.541 0.668 0.3932 0.0266 0.0701 + 12SOL HW1 35 0.375 0.512 0.588 -1.0573 0.7112 0.7694 + 12SOL HW2 36 0.376 0.610 0.718 1.2841 -0.4324 1.6239 + 13SOL OW 37 1.496 0.946 1.174 0.0346 0.2886 -0.0683 + 13SOL HW1 38 1.555 0.868 1.153 3.0420 2.1648 1.4208 + 13SOL HW2 39 1.463 0.987 1.089 -0.1563 -1.5776 -0.8770 + 14SOL OW 40 1.416 1.196 0.728 -0.0776 -0.1182 0.4006 + 14SOL HW1 41 1.404 1.294 0.712 -0.3229 -0.0522 0.9770 + 14SOL HW2 42 1.482 1.159 0.663 -0.8257 0.2139 -0.5386 + 15SOL OW 43 0.619 0.002 0.834 -0.2858 -0.1548 -0.0229 + 15SOL HW1 44 0.574 -0.005 0.923 1.0199 1.7395 0.7870 + 15SOL HW2 45 0.569 0.067 0.776 0.3399 0.5439 0.2231 + 16SOL OW 46 1.846 0.346 0.269 -0.1576 0.4363 -0.2770 + 16SOL HW1 47 1.761 0.394 0.293 1.3202 3.0558 -0.2747 + 16SOL HW2 48 1.885 0.305 0.351 0.3979 2.1575 0.3216 + 17SOL OW 49 0.693 0.116 1.701 -0.1420 0.3364 0.5550 + 17SOL HW1 50 0.693 0.123 1.800 0.4451 0.5853 0.5390 + 17SOL HW2 51 0.599 0.117 1.667 -0.3571 -0.3115 1.1484 + 18SOL OW 52 0.456 1.027 1.253 0.5076 0.9720 -0.1506 + 18SOL HW1 53 0.481 1.104 1.312 -1.6142 3.1862 -2.1560 + 18SOL HW2 54 0.376 0.981 1.291 0.7436 0.7893 0.1262 + 19SOL OW 55 1.527 1.386 1.708 -0.3078 0.2452 -0.6076 + 19SOL HW1 56 1.602 1.420 1.765 -1.6859 0.6806 0.9583 + 19SOL HW2 57 1.499 1.295 1.739 -3.1447 1.7876 1.4177 + 20SOL OW 58 1.006 0.850 1.021 0.7143 0.0855 -0.2086 + 20SOL HW1 59 0.985 0.762 1.062 0.1014 0.1228 -0.4349 + 20SOL HW2 60 0.997 0.843 0.921 0.8754 0.3463 -0.2418 + 21SOL OW 61 0.847 0.985 0.318 0.2013 0.1516 0.0950 + 21SOL HW1 62 0.778 1.046 0.280 -1.3473 -1.9024 -0.3641 + 21SOL HW2 63 0.828 0.969 0.415 -0.6862 -1.4146 -0.3339 + 22SOL OW 64 1.736 1.128 0.100 -0.0597 -0.1567 -0.5288 + 22SOL HW1 65 1.730 1.057 0.170 -3.1634 0.6867 0.0490 + 22SOL HW2 66 1.704 1.091 0.012 -2.6816 0.8293 0.0021 + 23SOL OW 67 1.673 0.501 0.733 -0.4629 0.0376 0.4769 + 23SOL HW1 68 1.650 0.438 0.660 -1.8167 -0.6912 1.5265 + 23SOL HW2 69 1.752 0.557 0.706 -2.5829 1.5470 -2.5385 + 24SOL OW 70 1.556 1.730 1.574 -0.4708 0.1404 -0.0011 + 24SOL HW1 71 1.654 1.717 1.580 -0.7732 -1.8162 0.6214 + 24SOL HW2 72 1.514 1.651 1.528 -1.7357 0.9824 -0.3106 + 25SOL OW 73 0.253 1.337 1.344 -0.2351 -0.2952 -0.4891 + 25SOL HW1 74 0.331 1.300 1.395 0.5926 1.5976 -0.3748 + 25SOL HW2 75 0.283 1.415 1.290 -1.5932 -0.9614 -2.1874 + 26SOL OW 76 1.446 1.139 0.410 -0.2590 -0.1564 -0.4546 + 26SOL HW1 77 1.393 1.177 0.334 0.5606 0.0896 -0.9011 + 26SOL HW2 78 1.477 1.047 0.386 -0.4790 -0.2957 -0.1982 + 27SOL OW 79 1.225 1.804 0.579 0.4112 -0.4666 0.3922 + 27SOL HW1 80 1.158 1.876 0.590 -1.2163 -1.9670 0.2386 + 27SOL HW2 81 1.187 1.717 0.611 2.0713 -1.4152 -0.1924 + 28SOL OW 82 1.697 1.262 1.165 -0.4609 -0.1360 0.4100 + 28SOL HW1 83 1.787 1.226 1.189 -0.1844 -0.0195 -0.4533 + 28SOL HW2 84 1.698 1.362 1.171 -0.3410 -0.1010 -0.3069 + 29SOL OW 85 0.579 0.785 1.158 -0.6039 0.0027 0.1263 + 29SOL HW1 86 0.605 0.805 1.064 -1.7650 0.9160 0.0045 + 29SOL HW2 87 0.538 0.866 1.200 0.3336 -0.2568 1.5645 + 30SOL OW 88 0.189 1.181 0.904 0.1349 0.0863 0.0035 + 30SOL HW1 89 0.275 1.191 0.954 0.3080 0.7337 -0.4215 + 30SOL HW2 90 0.158 1.086 0.909 0.7650 -0.0993 0.3367 + 31SOL OW 91 0.072 1.404 0.836 -0.0519 -0.4106 -0.0566 + 31SOL HW1 92 0.112 1.312 0.847 1.8201 0.3695 -0.3395 + 31SOL HW2 93 -0.023 1.403 0.869 -0.2430 -2.6121 -0.6532 + 32SOL OW 94 0.994 1.652 1.766 0.3962 0.2266 0.3655 + 32SOL HW1 95 1.051 1.608 1.697 0.3360 0.8117 -0.0588 + 32SOL HW2 96 1.044 1.730 1.805 1.0214 -1.0232 2.0486 + 33SOL OW 97 1.853 0.024 0.098 0.3529 -0.0632 -0.2369 + 33SOL HW1 98 1.766 0.072 0.101 -0.0894 -0.9848 1.8098 + 33SOL HW2 99 1.837 -0.075 0.095 1.3032 -0.1909 -1.6460 + 34SOL OW 100 1.170 1.086 0.680 -0.5290 0.4186 -0.2388 + 34SOL HW1 101 1.114 1.123 0.754 -0.6259 0.1726 -0.1901 + 34SOL HW2 102 1.266 1.108 0.696 -0.5839 0.6332 -0.1995 + 35SOL OW 103 0.160 0.673 1.029 0.5353 -0.6360 0.2722 + 35SOL HW1 104 0.099 0.599 1.001 -0.3914 0.0722 0.4051 + 35SOL HW2 105 0.175 0.668 1.128 0.7066 -0.8246 0.2358 + 36SOL OW 106 1.539 0.232 0.865 0.4243 0.2788 0.9219 + 36SOL HW1 107 1.516 0.136 0.852 1.5673 0.0640 0.4580 + 36SOL HW2 108 1.466 0.289 0.828 -0.4446 -0.4188 1.5737 + 37SOL OW 109 0.606 1.534 1.648 -0.1755 -0.6691 0.5412 + 37SOL HW1 110 0.510 1.557 1.667 0.4807 0.1002 2.8682 + 37SOL HW2 111 0.658 1.619 1.633 0.9139 -0.9373 2.8640 + 38SOL OW 112 0.165 0.204 1.528 0.4198 -0.2931 0.8233 + 38SOL HW1 113 0.105 0.268 1.482 -1.1008 -2.9191 -0.8558 + 38SOL HW2 114 0.144 0.201 1.625 -0.2313 0.9300 0.7121 + 39SOL OW 115 1.008 0.126 0.568 0.4090 -0.3739 0.1418 + 39SOL HW1 116 0.948 0.175 0.631 0.5784 0.4007 -0.3058 + 39SOL HW2 117 0.955 0.063 0.512 0.1202 -0.2579 0.2894 + 40SOL OW 118 1.113 1.270 1.543 -0.1267 -0.1716 0.1304 + 40SOL HW1 119 1.181 1.282 1.615 -0.6890 1.3225 0.4068 + 40SOL HW2 120 1.150 1.210 1.472 0.6213 -1.2290 1.4023 + 41SOL OW 121 1.840 0.850 1.758 0.2653 0.2874 0.7400 + 41SOL HW1 122 1.771 0.921 1.740 0.2976 -0.3205 -1.8404 + 41SOL HW2 123 1.931 0.892 1.755 0.0539 0.9551 3.4538 + 42SOL OW 124 1.205 0.990 1.178 0.0610 -0.1458 0.1747 + 42SOL HW1 125 1.136 0.927 1.142 0.6332 0.0555 -1.2591 + 42SOL HW2 126 1.270 1.014 1.106 1.3999 -0.0050 1.4122 + 43SOL OW 127 1.124 0.665 0.133 -0.0861 -0.3223 -0.3257 + 43SOL HW1 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49SOL HW1 146 1.447 0.142 1.329 0.1750 -0.5611 -0.4432 + 49SOL HW2 147 1.510 0.030 1.429 0.1635 -0.1394 0.0389 + 50SOL OW 148 1.012 1.117 0.886 0.4322 0.6891 0.1644 + 50SOL HW1 149 0.997 1.050 0.959 2.5811 -2.2474 -2.0740 + 50SOL HW2 150 0.968 1.203 0.910 -1.1948 -1.1284 3.6840 + 51SOL OW 151 0.711 0.119 0.415 -0.1656 0.0551 0.2223 + 51SOL HW1 152 0.774 0.189 0.447 -0.8893 0.3597 0.9889 + 51SOL HW2 153 0.618 0.155 0.417 -0.5471 -0.9545 0.7128 + 52SOL OW 154 1.410 1.445 0.231 0.4389 0.3169 0.8853 + 52SOL HW1 155 1.357 1.526 0.257 0.3606 1.2478 -2.1842 + 52SOL HW2 156 1.349 1.367 0.219 0.3700 0.1068 2.5878 + 53SOL OW 157 1.658 0.375 1.825 0.2207 -0.1764 0.0443 + 53SOL HW1 158 1.623 0.372 1.731 0.8986 0.2393 -0.2204 + 53SOL HW2 159 1.754 0.403 1.824 0.4825 -1.0439 0.7931 + 54SOL OW 160 0.690 0.449 0.985 -0.0672 0.5058 0.1969 + 54SOL HW1 161 0.719 0.544 0.967 -1.4982 1.2210 1.6269 + 54SOL HW2 162 0.590 0.446 0.993 -0.0410 -1.2007 -0.2987 + 55SOL OW 163 1.423 0.526 1.363 -0.1904 0.2178 0.1867 + 55SOL HW1 164 1.417 0.434 1.400 1.0790 0.0457 -0.0544 + 55SOL HW2 165 1.488 0.580 1.417 -1.4149 1.1675 0.7350 + 56SOL OW 166 0.383 0.196 0.100 -0.7297 -0.3771 -0.7214 + 56SOL HW1 167 0.316 0.188 0.027 -0.1773 -1.6716 -1.1026 + 56SOL HW2 168 0.440 0.113 0.101 -0.8614 -0.4436 1.2761 + 57SOL OW 169 0.044 0.315 0.548 -0.5611 -0.3874 -0.2822 + 57SOL HW1 170 -0.027 0.379 0.519 0.3940 0.3906 -0.8864 + 57SOL HW2 171 0.007 0.254 0.618 -0.7588 2.3062 1.9556 + 58SOL OW 172 0.779 1.711 0.210 0.0185 -0.2193 -0.3148 + 58SOL HW1 173 0.861 1.767 0.203 -0.2747 0.0369 -1.8401 + 58SOL HW2 174 0.740 1.720 0.301 -0.3824 2.5490 -0.7565 + 59SOL OW 175 0.710 0.747 0.411 -0.2726 -0.4241 -0.4418 + 59SOL HW1 176 0.649 0.715 0.338 0.5813 -0.9072 -0.9452 + 59SOL HW2 177 0.783 0.803 0.372 -1.3479 1.5382 0.3653 + 60SOL OW 178 1.362 0.718 1.859 0.0661 -0.0068 0.3879 + 60SOL HW1 179 1.353 0.709 1.760 0.1108 1.1820 0.2772 + 60SOL HW2 180 1.275 0.694 1.903 0.1612 -0.9038 0.0861 + 61SOL OW 181 1.681 1.337 0.889 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b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/ener.edr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/md.log b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/md.log new file mode 100644 index 00000000..02b442ca --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/md.log @@ -0,0 +1,483 @@ +Log file opened on Wed Jan 3 15:00:40 2024 +Host: FAIRmat-AreaC2-Rudzinski pid: 389844 rank ID: 0 number of ranks: 1 + :-) GROMACS - gmx mdrun, 2018.6 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra + Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru + Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus + Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl + Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola + Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov + Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2017, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2018.6 +Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_integrators_1frame/md-vv +Command line: + gmx mdrun -s water.tpr -o water.trr + +GROMACS version: 2018.6 +Precision: single +Memory model: 64 bit +MPI library: thread_mpi +OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) +GPU support: OpenCL +SIMD instructions: SSE2 +FFT library: fftw-3.3.8-sse2-avx +RDTSCP usage: disabled +TNG support: enabled +Hwloc support: hwloc-1.11.9 +Tracing support: disabled +Built on: 2019-05-12 20:18:02 +Built by: root@default-0e84dd72-7298-44a4-a670-e10728e370dd [CMAKE] +Build OS/arch: Linux 4.4.0-96-generic x86_64 +Build CPU vendor: Unknown +Build CPU brand: Unknown +Build CPU family: 0 Model: 0 Stepping: 0 +Build CPU features: Unknown +C compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc GNU 7.3.0 +C compiler flags: -msse2 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +C++ compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ GNU 7.3.0 +C++ compiler flags: -msse2 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +OpenCL include dir: /home/jfrudzinski/miniconda3/envs/martignac_2/include +OpenCL library: /home/jfrudzinski/miniconda3/envs/martignac_2/lib/libOpenCL.so +OpenCL version: 2.0 + +NOTE: Detection of GPUs failed. The API reported: + GROMACS cannot run tasks on a GPU. + +Running on 1 node with total 4 cores, 8 logical cores, 0 compatible GPUs +Hardware detected: + CPU info: + Vendor: Intel + Brand: 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz + Family: 6 Model: 140 Stepping: 1 + Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic + Number of AVX-512 FMA units: Cannot run AVX-512 detection - assuming 2 + Hardware topology: Full, with devices + Sockets, cores, and logical processors: + Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] + Numa nodes: + Node 0 (16138244096 bytes mem): 0 1 2 3 4 5 6 7 + Latency: + 0 + 0 1.00 + Caches: + L1: 49152 bytes, linesize 64 bytes, assoc. 12, shared 2 ways + L2: 1310720 bytes, linesize 64 bytes, assoc. 20, shared 2 ways + L3: 12582912 bytes, linesize 64 bytes, assoc. 12, shared 8 ways + PCI devices: + 0000:00:02.0 Id: 8086:9a49 Class: 0x0300 Numa: 0 + 0000:00:0e.0 Id: 8086:9a0b Class: 0x0104 Numa: 0 + 0000:00:14.3 Id: 8086:a0f0 Class: 0x0280 Numa: 0 + 0000:00:1f.6 Id: 8086:15fb Class: 0x0200 Numa: 0 + +Highest SIMD level requested by all nodes in run: AVX_512 +SIMD instructions selected at compile time: SSE2 +This program was compiled for different hardware than you are running on, +which could influence performance. + +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. +Lindahl +GROMACS: High performance molecular simulations through multi-level +parallelism from laptops to supercomputers +SoftwareX 1 (2015) pp. 19-25 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl +Tackling Exascale Software Challenges in Molecular Dynamics Simulations with +GROMACS +In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. +Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl +GROMACS 4.5: a high-throughput and highly parallel open source molecular +simulation toolkit +Bioinformatics 29 (2013) pp. 845-54 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl +GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable +molecular simulation +J. Chem. Theory Comput. 4 (2008) pp. 435-447 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. +Berendsen +GROMACS: Fast, Flexible and Free +J. Comp. Chem. 26 (2005) pp. 1701-1719 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +E. Lindahl and B. Hess and D. van der Spoel +GROMACS 3.0: A package for molecular simulation and trajectory analysis +J. Mol. Mod. 7 (2001) pp. 306-317 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +H. J. C. Berendsen, D. van der Spoel and R. van Drunen +GROMACS: A message-passing parallel molecular dynamics implementation +Comp. Phys. Comm. 91 (1995) pp. 43-56 +-------- -------- --- Thank You --- -------- -------- + +Input Parameters: + integrator = md-vv + tinit = 0 + dt = 0.001 + nsteps = 1 + init-step = 0 + simulation-part = 1 + comm-mode = Linear + nstcomm = 1 + bd-fric = 0 + ld-seed = 1902240194 + emtol = 10 + emstep = 0.01 + niter = 20 + fcstep = 0 + nstcgsteep = 1000 + nbfgscorr = 10 + rtpi = 0.05 + nstxout = 1 + nstvout = 1 + nstfout = 1 + nstlog = 1 + nstcalcenergy = 1 + nstenergy = 1 + nstxout-compressed = 0 + compressed-x-precision = 1000 + cutoff-scheme = Verlet + nstlist = 1 + ns-type = Grid + pbc = xyz + periodic-molecules = false + verlet-buffer-tolerance = 0.005 + rlist = 0.9 + coulombtype = PME + coulomb-modifier = Potential-shift + rcoulomb-switch = 0 + rcoulomb = 0.9 + epsilon-r = 1 + epsilon-rf = inf + vdw-type = Cut-off + vdw-modifier = Potential-shift + rvdw-switch = 0 + rvdw = 0.9 + DispCorr = EnerPres + table-extension = 1 + fourierspacing = 0.08 + fourier-nx = 24 + fourier-ny = 24 + fourier-nz = 24 + pme-order = 6 + ewald-rtol = 1e-06 + ewald-rtol-lj = 0.001 + lj-pme-comb-rule = Geometric + ewald-geometry = 0 + epsilon-surface = 0 + implicit-solvent = No + gb-algorithm = Still + nstgbradii = 1 + rgbradii = 1 + gb-epsilon-solvent = 80 + gb-saltconc = 0 + gb-obc-alpha = 1 + gb-obc-beta = 0.8 + gb-obc-gamma = 4.85 + gb-dielectric-offset = 0.009 + sa-algorithm = Ace-approximation + sa-surface-tension = 2.05016 + tcoupl = No + nsttcouple = -1 + nh-chain-length = 0 + print-nose-hoover-chain-variables = false + pcoupl = No + pcoupltype = Isotropic + nstpcouple = -1 + tau-p = 1 + compressibility (3x3): + compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p (3x3): + ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + refcoord-scaling = No + posres-com (3): + posres-com[0]= 0.00000e+00 + posres-com[1]= 0.00000e+00 + posres-com[2]= 0.00000e+00 + posres-comB (3): + posres-comB[0]= 0.00000e+00 + posres-comB[1]= 0.00000e+00 + posres-comB[2]= 0.00000e+00 + QMMM = false + QMconstraints = 0 + QMMMscheme = 0 + MMChargeScaleFactor = 1 +qm-opts: + ngQM = 0 + constraint-algorithm = Lincs + continuation = false + Shake-SOR = false + shake-tol = 0.0001 + lincs-order = 4 + lincs-iter = 1 + lincs-warnangle = 30 + nwall = 0 + wall-type = 9-3 + wall-r-linpot = -1 + wall-atomtype[0] = -1 + wall-atomtype[1] = -1 + wall-density[0] = 0 + wall-density[1] = 0 + wall-ewald-zfac = 3 + pull = false + awh = false + rotation = false + interactiveMD = false + disre = No + disre-weighting = Conservative + disre-mixed = false + dr-fc = 1000 + dr-tau = 0 + nstdisreout = 100 + orire-fc = 0 + orire-tau = 0 + nstorireout = 100 + free-energy = no + cos-acceleration = 0 + deform (3x3): + deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + simulated-tempering = false + swapcoords = no + userint1 = 0 + userint2 = 0 + userint3 = 0 + userint4 = 0 + userreal1 = 0 + userreal2 = 0 + userreal3 = 0 + userreal4 = 0 + applied-forces: + electric-field: + x: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + y: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + z: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 +grpopts: + nrdf: 1293 + ref-t: 0 + tau-t: 0 +annealing: No +annealing-npoints: 0 + acc: 0 0 0 + nfreeze: N N N + energygrp-flags[ 0]: 0 + + +Using 1 MPI thread +Using 8 OpenMP threads + +Pinning threads with an auto-selected logical core stride of 1 +System total charge: 0.000 +Will do PME sum in reciprocal space for electrostatic interactions. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen +A smooth particle mesh Ewald method +J. Chem. Phys. 103 (1995) pp. 8577-8592 +-------- -------- --- Thank You --- -------- -------- + +Using a Gaussian width (1/beta) of 0.260197 nm for Ewald +Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-06 +Initialized non-bonded Ewald correction tables, spacing: 8.41e-04 size: 1071 + +Long Range LJ corr.: 2.9078e-04 +Generated table with 950 data points for Ewald. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ6. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ12. +Tabscale = 500 points/nm + +Using SIMD 4x4 nonbonded short-range kernels + +Using a 4x4 pair-list setup: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm + +Using geometric Lennard-Jones combination rule + +Removing pbc first time + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Miyamoto and P. A. Kollman +SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid +Water Models +J. Comp. Chem. 13 (1992) pp. 952-962 +-------- -------- --- Thank You --- -------- -------- + + +Intra-simulation communication will occur every 1 steps. +Center of mass motion removal mode is Linear +We have the following groups for center of mass motion removal: + 0: rest +There are: 648 Atoms + +Constraining the starting coordinates (step 0) +RMS relative constraint deviation after constraining: 0.00e+00 +Initial temperature: 298.999 K + +Started mdrun on rank 0 Wed Jan 3 15:00:41 2024 + Step Time + 0 0.00000 + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.98181e+03 -1.08747e+02 -1.21912e+04 1.28385e+02 -1.01898e+04 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.60721e+03 -8.58255e+03 2.98999e+02 -2.80811e+02 -5.26261e+02 + + Step Time + 1 0.00100 + +Writing checkpoint, step 1 at Wed Jan 3 15:00:41 2024 + + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97910e+03 -1.08747e+02 -1.21940e+04 1.25188e+02 -1.01984e+04 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.61583e+03 -8.58260e+03 3.00603e+02 -2.80811e+02 -5.72191e+02 + + <====== ############### ==> + <==== A V E R A G E S ====> + <== ############### ======> + + Statistics over 2 steps using 2 frames + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.98045e+03 -1.08747e+02 -1.21926e+04 1.26787e+02 -1.01941e+04 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.61152e+03 -8.58257e+03 2.99801e+02 -2.80811e+02 -5.49226e+02 + + Total Virial (kJ/mol) + 6.63185e+02 1.15696e+02 1.47088e+02 + 1.16501e+02 5.71502e+02 -7.05956e+00 + 1.47482e+02 -6.82181e+00 6.96392e+02 + + Pressure (bar) + -7.55702e+02 -5.09752e+02 -6.18004e+02 + -5.13902e+02 -3.57840e+02 7.75691e+01 + -6.20032e+02 7.63433e+01 -5.34135e+02 + + + M E G A - F L O P S A C C O U N T I N G + + NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels + RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table + W3=SPC/TIP3p W4=TIP4p (single or pairs) + V&F=Potential and force V=Potential only F=Force only + + Computing: M-Number M-Flops % Flops +----------------------------------------------------------------------------- + Pair Search distance check 0.304450 2.740 8.5 + NxN QSTab Elec. + LJ [V&F] 0.205992 12.154 37.9 + NxN QSTab Elec. [V&F] 0.198216 8.127 25.3 + Calc Weights 0.003888 0.140 0.4 + Spread Q Bspline 0.279936 0.560 1.7 + Gather F Bspline 0.279936 1.680 5.2 + 3D-FFT 0.760588 6.085 19.0 + Solve PME 0.001152 0.074 0.2 + Shift-X 0.001296 0.008 0.0 + Virial 0.001386 0.025 0.1 + Stop-CM 0.001944 0.019 0.1 + Calc-Ekin 0.001296 0.035 0.1 + Constraint-V 0.001296 0.010 0.0 + Constraint-Vir 0.001296 0.031 0.1 + Settle 0.001296 0.419 1.3 +----------------------------------------------------------------------------- + Total 32.106 100.0 +----------------------------------------------------------------------------- + + + R E A L C Y C L E A N D T I M E A C C O U N T I N G + +On 1 MPI rank, each using 8 OpenMP threads + + Computing: Num Num Call Wall time Giga-Cycles + Ranks Threads Count (s) total sum % +----------------------------------------------------------------------------- + Neighbor search 1 8 2 0.001 0.011 1.2 + Force 1 8 2 0.000 0.004 0.4 + PME mesh 1 8 2 0.000 0.005 0.5 + NB X/F buffer ops. 1 8 2 0.000 0.000 0.0 + Write traj. 1 8 2 0.039 0.559 62.1 + Update 1 8 8 0.021 0.310 34.4 + Constraints 1 8 4 0.000 0.000 0.0 + Rest 0.001 0.012 1.4 +----------------------------------------------------------------------------- + Total 0.062 0.901 100.0 +----------------------------------------------------------------------------- + Breakdown of PME mesh computation +----------------------------------------------------------------------------- + PME spread 1 8 2 0.000 0.002 0.2 + PME gather 1 8 2 0.000 0.001 0.1 + PME 3D-FFT 1 8 4 0.000 0.001 0.1 + PME solve Elec 1 8 2 0.000 0.000 0.1 +----------------------------------------------------------------------------- + + Core t (s) Wall t (s) (%) + Time: 0.499 0.062 800.0 + (ns/day) (hour/ns) +Performance: 2.770 8.665 +Finished mdrun on rank 0 Wed Jan 3 15:00:41 2024 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/mdout.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/mdout.mdp new file mode 100644 index 00000000..6e80948e --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/mdout.mdp @@ -0,0 +1,353 @@ +; +; File 'mdout.mdp' was generated +; By user: jfrudzinski (1000) +; On host: FAIRmat-AreaC2-Rudzinski +; At date: Wed Jan 3 15:00:40 2024 +; +; Created by: +; :-) GROMACS - gmx grompp, 2018.6 (-: +; +; Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +; Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +; Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/water_AA_integrators_1frame/md-vv +; Command line: +; gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +; VARIOUS PREPROCESSING OPTIONS +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/roe +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ +; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) +define = + +; RUN CONTROL PARAMETERS +integrator = md-vv +; Start time and timestep in ps +tinit = 0.0 +dt = 0.001 +nsteps = 1 +; For exact run continuation or redoing part of a run +init-step = 0 +; Part index is updated automatically on checkpointing (keeps files separate) +simulation-part = 1 +; mode for center of mass motion removal +comm-mode = linear +; number of steps for center of mass motion removal +nstcomm = 1 +; group(s) for center of mass motion removal +comm-grps = + +; LANGEVIN DYNAMICS OPTIONS +; Friction coefficient (amu/ps) and random seed +bd-fric = 0 +ld-seed = -1 + +; ENERGY MINIMIZATION OPTIONS +; Force tolerance and initial step-size +emtol = 10 +emstep = 0.01 +; Max number of iterations in relax-shells +niter = 20 +; Step size (ps^2) for minimization of flexible constraints +fcstep = 0 +; Frequency of steepest descents steps when doing CG +nstcgsteep = 1000 +nbfgscorr = 10 + +; TEST PARTICLE INSERTION OPTIONS +rtpi = 0.05 + +; OUTPUT CONTROL OPTIONS +; Output frequency for coords (x), velocities (v) and forces (f) +nstxout = 1 +nstvout = 1 +nstfout = 1 +; Output frequency for energies to log file and energy file +nstlog = 1 +nstcalcenergy = 100 +nstenergy = 1 +; Output frequency and precision for .xtc file +nstxout-compressed = 0 +compressed-x-precision = 1000 +; This selects the subset of atoms for the compressed +; trajectory file. You can select multiple groups. By +; default, all atoms will be written. +compressed-x-grps = +; Selection of energy groups +energygrps = System + +; NEIGHBORSEARCHING PARAMETERS +; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) +cutoff-scheme = Verlet +; nblist update frequency +nstlist = 1 +; ns algorithm (simple or grid) +ns_type = grid +; Periodic boundary conditions: xyz, no, xy +pbc = xyz +periodic-molecules = no +; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, +; a value of -1 means: use rlist +verlet-buffer-tolerance = 0.005 +; nblist cut-off +rlist = 0.9 +; long-range cut-off for switched potentials + +; OPTIONS FOR ELECTROSTATICS AND VDW +; Method for doing electrostatics +coulombtype = PME +coulomb-modifier = Potential-shift-Verlet +rcoulomb-switch = 0 +rcoulomb = 0.9 +; Relative dielectric constant for the medium and the reaction field +epsilon-r = 1 +epsilon-rf = 0 +; Method for doing Van der Waals +vdwtype = cutoff +vdw-modifier = Potential-shift-Verlet +; cut-off lengths +rvdw-switch = 0 +rvdw = 0.9 +; Apply long range dispersion corrections for Energy and Pressure +DispCorr = EnerPres +; Extension of the potential lookup tables beyond the cut-off +table-extension = 1 +; Separate tables between energy group pairs +energygrp-table = +; Spacing for the PME/PPPM FFT grid +fourierspacing = 0.08 +; FFT grid size, when a value is 0 fourierspacing will be used +fourier-nx = 0 +fourier-ny = 0 +fourier-nz = 0 +; EWALD/PME/PPPM parameters +pme_order = 6 +ewald_rtol = 1e-06 +ewald-rtol-lj = 0.001 +lj-pme-comb-rule = Geometric +ewald-geometry = 3d +epsilon-surface = 0 + +; IMPLICIT SOLVENT ALGORITHM +implicit-solvent = No + +; GENERALIZED BORN ELECTROSTATICS +; Algorithm for calculating Born radii +gb-algorithm = Still +; Frequency of calculating the Born radii inside rlist +nstgbradii = 1 +; Cutoff for Born radii calculation; the contribution from atoms +; between rlist and rgbradii is updated every nstlist steps +rgbradii = 1 +; Dielectric coefficient of the implicit solvent +gb-epsilon-solvent = 80 +; Salt concentration in M for Generalized Born models +gb-saltconc = 0 +; Scaling factors used in the OBC GB model. Default values are OBC(II) +gb-obc-alpha = 1 +gb-obc-beta = 0.8 +gb-obc-gamma = 4.85 +gb-dielectric-offset = 0.009 +sa-algorithm = Ace-approximation +; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA +; The value -1 will set default value for Still/HCT/OBC GB-models. +sa-surface-tension = -1 + +; OPTIONS FOR WEAK COUPLING ALGORITHMS +; Temperature coupling +tcoupl = No +nsttcouple = -1 +nh-chain-length = 10 +print-nose-hoover-chain-variables = no +; Groups to couple separately +tc_grps = System +; Time constant (ps) and reference temperature (K) +tau_t = 0.5 +ref_t = 298 +; pressure coupling +pcoupl = No +pcoupltype = Isotropic +nstpcouple = -1 +; Time constant (ps), compressibility (1/bar) and reference P (bar) +tau-p = 1 +compressibility = +ref-p = +; Scaling of reference coordinates, No, All or COM +refcoord-scaling = No + +; OPTIONS FOR QMMM calculations +QMMM = no +; Groups treated Quantum Mechanically +QMMM-grps = +; QM method +QMmethod = +; QMMM scheme +QMMMscheme = normal +; QM basisset +QMbasis = +; QM charge +QMcharge = +; QM multiplicity +QMmult = +; Surface Hopping +SH = +; CAS space options +CASorbitals = +CASelectrons = +SAon = +SAoff = +SAsteps = +; Scale factor for MM charges +MMChargeScaleFactor = 1 + +; SIMULATED ANNEALING +; Type of annealing for each temperature group (no/single/periodic) +annealing = +; Number of time points to use for specifying annealing in each group +annealing-npoints = +; List of times at the annealing points for each group +annealing-time = +; Temp. at each annealing point, for each group. +annealing-temp = + +; GENERATE VELOCITIES FOR STARTUP RUN +gen_vel = yes +gen_temp = 298 +gen_seed = 173529 + +; OPTIONS FOR BONDS +constraints = none +; Type of constraint algorithm +constraint-algorithm = Lincs +; Do not constrain the start configuration +continuation = no +; Use successive overrelaxation to reduce the number of shake iterations +Shake-SOR = no +; Relative tolerance of shake +shake-tol = 0.0001 +; Highest order in the expansion of the constraint coupling matrix +lincs-order = 4 +; Number of iterations in the final step of LINCS. 1 is fine for +; normal simulations, but use 2 to conserve energy in NVE runs. +; For energy minimization with constraints it should be 4 to 8. +lincs-iter = 1 +; Lincs will write a warning to the stderr if in one step a bond +; rotates over more degrees than +lincs-warnangle = 30 +; Convert harmonic bonds to morse potentials +morse = no + +; ENERGY GROUP EXCLUSIONS +; Pairs of energy groups for which all non-bonded interactions are excluded +energygrp-excl = + +; WALLS +; Number of walls, type, atom types, densities and box-z scale factor for Ewald +nwall = 0 +wall-type = 9-3 +wall-r-linpot = -1 +wall-atomtype = +wall-density = +wall-ewald-zfac = 3 + +; COM PULLING +pull = no + +; AWH biasing +awh = no + +; ENFORCED ROTATION +; Enforced rotation: No or Yes +rotation = no + +; Group to display and/or manipulate in interactive MD session +IMD-group = + +; NMR refinement stuff +; Distance restraints type: No, Simple or Ensemble +disre = No +; Force weighting of pairs in one distance restraint: Conservative or Equal +disre-weighting = Conservative +; Use sqrt of the time averaged times the instantaneous violation +disre-mixed = no +disre-fc = 1000 +disre-tau = 0 +; Output frequency for pair distances to energy file +nstdisreout = 100 +; Orientation restraints: No or Yes +orire = no +; Orientation restraints force constant and tau for time averaging +orire-fc = 0 +orire-tau = 0 +orire-fitgrp = +; Output frequency for trace(SD) and S to energy file +nstorireout = 100 + +; Free energy variables +free-energy = no +couple-moltype = +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q +couple-intramol = no +init-lambda = -1 +init-lambda-state = -1 +delta-lambda = 0 +nstdhdl = 50 +fep-lambdas = +mass-lambdas = +coul-lambdas = +vdw-lambdas = +bonded-lambdas = +restraint-lambdas = +temperature-lambdas = +calc-lambda-neighbors = 1 +init-lambda-weights = +dhdl-print-energy = no +sc-alpha = 0 +sc-power = 1 +sc-r-power = 6 +sc-sigma = 0.3 +sc-coul = no +separate-dhdl-file = yes +dhdl-derivatives = yes +dh_hist_size = 0 +dh_hist_spacing = 0.1 + +; Non-equilibrium MD stuff +acc-grps = +accelerate = +freezegrps = +freezedim = +cos-acceleration = 0 +deform = + +; simulated tempering variables +simulated-tempering = no +simulated-tempering-scaling = geometric +sim-temp-low = 300 +sim-temp-high = 300 + +; Ion/water position swapping for computational electrophysiology setups +; Swap positions along direction: no, X, Y, Z +swapcoords = no +adress = no + +; User defined thingies +user1-grps = +user2-grps = +userint1 = 0 +userint2 = 0 +userint3 = 0 +userint4 = 0 +userreal1 = 0 +userreal2 = 0 +userreal3 = 0 +userreal4 = 0 +; Electric fields +; Format for electric-field-x, etc. is: four real variables: +; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), +; and sigma (ps) width of the pulse. Omega = 0 means static field, +; sigma = 0 means no pulse, leaving the field to be a cosine function. +electric-field-x = 0 0 0 0 +electric-field-y = 0 0 0 0 +electric-field-z = 0 0 0 0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/state.cpt b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/state.cpt new file mode 100644 index 00000000..3e9e8cb1 Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/state.cpt differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.298.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.298.mdp new file mode 100644 index 00000000..354c2e0a --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.298.mdp @@ -0,0 +1,52 @@ +; Preprocessing +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ + +; Run Control +integrator = md-vv +tinit = 0.0 +dt = 0.001 ; 1.0 fs +nsteps = 1 ; 20 ns +nstcomm = 1 ; no. steps between removing com motion +comm-mode = linear ; remove com translation + +; Output Control +nstxout = 1 ; no. steps between printing coords to trr file => 1ps +nstvout = 1 ; no. steps between printing veloc to trr file +nstfout = 1 ; no. steps between printing forces to trr file => 1ps +nstlog = 1 ; no. steps between printing energy to log file => 1ps +nstenergy = 1 ; no. steps between printing energy to edr file => 1ps +nstxtcout = 0 ; no. stpes between printing coords to xtc file +energygrps = System ; groups for writing energy file + +; Neighbor searching +nstlist = 1 ; update neighbor list every step +ns_type = grid ; check neighbor list using grid +rlist = 0.9 ; cutoff distance (nm) for short-range neighbor list + +; Electrostatics and VdW +coulombtype = PME ; fast particle-mesh ewald electrostatics +rcoulomb = 0.9 ; distance for the Coulomb cut-off +vdwtype = cutoff ; truncated LJ interactions +rvdw = 0.9 ; distance for LJ cut-off +DispCorr = EnerPres ; apply long range disp. correct. for Energy/Pres +fourierspacing = 0.08 ; max grid spacing fr FFT grid in PME +pme_order = 6 ; interpolation order for PME +ewald_rtol = 1e-06 ; relative strength of direct potential at cutoff +optimize_fft = yes ; optimize fft_grids + +; Temperature Coupling +;tcoupl = nose-hoover ; nose-hoover for correct ensemble +tc_grps = System ; groups to couple separtly to temp. bath +tau_t = 0.5 ; time constant for coupling +ref_t = 298 ; ref. temperature for coupling + +; Velocity generation +gen_vel = yes ; generate velocities with Max. dist. +gen_temp = 298 ; temp. for Max. dist. +gen_seed = 173529 ; for random number generator + +; Pressure coupling +;pcoupl = Parrinello-Rahman +;tau-p = 5.0 +;compressibility = 7.4e-5 +;ref-p = 1.0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.confout.gro new file mode 100644 index 00000000..0244d504 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.427 0.087 1.634 0.0670 0.6261 -0.3260 + 1SOL HW1 2 0.352 0.153 1.636 -0.6525 -0.2083 0.2628 + 1SOL HW2 3 0.394 -0.001 1.600 1.0005 0.5272 -1.0056 + 2SOL OW 4 0.365 0.990 0.648 0.2321 -0.9063 -0.2980 + 2SOL HW1 5 0.377 0.914 0.584 -0.7093 -1.6057 0.3416 + 2SOL HW2 6 0.274 1.030 0.635 -0.0303 -1.1620 0.7020 + 3SOL OW 7 1.293 1.628 1.682 0.0780 0.2611 -0.6033 + 3SOL HW1 8 1.334 1.698 1.741 0.7308 -0.2019 -0.4969 + 3SOL HW2 9 1.365 1.565 1.651 -0.3690 0.1198 -1.3618 + 4SOL OW 10 0.922 1.027 1.587 -0.3854 -0.0836 0.3470 + 4SOL HW1 11 0.948 1.121 1.565 0.9210 -0.3821 0.5298 + 4SOL HW2 12 0.938 1.009 1.684 -0.7039 -0.4697 0.3326 + 5SOL OW 13 0.871 1.326 0.395 -0.6365 0.2971 0.0566 + 5SOL HW1 14 0.954 1.367 0.432 -0.7776 -1.1407 2.0646 + 5SOL HW2 15 0.792 1.382 0.422 -0.5051 0.5885 -0.1623 + 6SOL OW 16 0.300 0.863 0.124 -0.1337 -0.5286 0.6475 + 6SOL HW1 17 0.252 0.908 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183SOL OW 547 0.286 0.097 1.177 0.5078 -0.0262 -0.1346 + 183SOL HW1 548 0.219 0.171 1.184 -0.0027 -0.3660 -1.2136 + 183SOL HW2 549 0.367 0.130 1.128 1.1385 0.3882 1.1809 + 184SOL OW 550 0.025 1.844 1.398 0.8241 0.0883 -0.4432 + 184SOL HW1 551 0.099 1.895 1.442 1.8365 -1.9952 0.2967 + 184SOL HW2 552 -0.012 1.776 1.461 -0.4736 -0.1561 -1.4373 + 185SOL OW 553 0.534 0.658 1.575 -0.3340 0.3639 -0.0368 + 185SOL HW1 554 0.574 0.664 1.667 0.3355 -1.0454 -0.2294 + 185SOL HW2 555 0.607 0.657 1.507 -0.6335 -2.9360 -0.3589 + 186SOL OW 556 1.418 0.775 0.820 -0.0169 1.0421 -0.8445 + 186SOL HW1 557 1.378 0.691 0.857 0.7531 1.3106 0.6462 + 186SOL HW2 558 1.398 0.782 0.723 -0.6095 -0.5640 -0.8452 + 187SOL OW 559 0.222 0.944 1.345 -0.2158 0.3297 -0.7016 + 187SOL HW1 560 0.131 0.904 1.335 -0.6758 0.9556 0.9203 + 187SOL HW2 561 0.226 0.999 1.428 1.2918 1.2851 -1.3770 + 188SOL OW 562 0.914 0.467 0.189 0.6525 0.6939 0.0840 + 188SOL HW1 563 0.871 0.549 0.227 -0.0617 0.1423 0.4674 + 188SOL HW2 564 0.873 0.447 0.100 0.4158 0.4051 0.2610 + 189SOL OW 565 0.801 1.764 1.597 0.0175 0.4390 0.1863 + 189SOL HW1 566 0.751 1.834 1.649 1.3774 1.6958 -0.1520 + 189SOL HW2 567 0.872 1.724 1.655 -0.2129 -0.0604 0.1199 + 190SOL OW 568 0.833 0.451 1.539 0.1980 0.3304 0.0083 + 190SOL HW1 569 0.803 0.547 1.533 -0.8407 0.1465 1.8404 + 190SOL HW2 570 0.929 0.444 1.510 0.6995 2.1522 1.1685 + 191SOL OW 571 1.110 0.916 0.220 0.1476 0.5001 -0.4889 + 191SOL HW1 572 1.129 0.820 0.200 -2.6997 0.4489 -3.4273 + 191SOL HW2 573 1.019 0.923 0.262 1.1175 1.7959 1.4857 + 192SOL OW 574 0.996 0.056 1.146 -0.0994 0.5545 0.4537 + 192SOL HW1 575 0.972 -0.004 1.222 -0.6136 1.3158 0.8946 + 192SOL HW2 576 0.960 0.148 1.162 1.8146 1.3433 0.4012 + 193SOL OW 577 0.514 1.254 1.408 0.1676 0.1755 -0.1092 + 193SOL HW1 578 0.528 1.208 1.496 -1.3291 -0.5253 -0.2132 + 193SOL HW2 579 0.601 1.288 1.374 0.7114 0.8100 1.8430 + 194SOL OW 580 1.424 1.837 1.808 0.0919 -0.5746 -0.2857 + 194SOL HW1 581 1.486 1.823 1.731 0.4877 1.9227 -0.4851 + 194SOL HW2 582 1.478 1.861 1.889 -0.4948 0.0238 -0.0653 + 195SOL OW 583 0.658 1.239 0.620 -0.3609 0.5478 -0.5495 + 195SOL HW1 584 0.747 1.197 0.604 -0.5919 0.8796 -2.7776 + 195SOL HW2 585 0.604 1.180 0.680 0.7884 -0.3959 -0.4194 + 196SOL OW 586 1.379 0.250 1.783 0.0082 -0.7042 0.3366 + 196SOL HW1 587 1.419 0.159 1.771 2.8172 0.8867 -3.3603 + 196SOL HW2 588 1.436 0.303 1.846 -0.5107 -0.8573 0.9364 + 197SOL OW 589 1.406 0.936 0.182 0.4528 -0.1813 0.0754 + 197SOL HW1 590 1.402 0.861 0.116 0.2006 -1.4207 1.4793 + 197SOL HW2 591 1.314 0.957 0.216 0.8623 -1.2400 1.8888 + 198SOL OW 592 0.030 0.412 1.436 0.2007 -0.0565 -0.4994 + 198SOL HW1 593 0.098 0.476 1.400 -0.3590 1.3329 0.8709 + 198SOL HW2 594 -0.018 0.453 1.513 -1.5666 -1.3714 -0.8498 + 199SOL OW 595 0.013 1.493 0.579 -0.5266 -0.7272 0.0410 + 199SOL HW1 596 0.039 1.479 0.675 -1.1788 1.6396 0.5768 + 199SOL HW2 597 -0.078 1.455 0.563 -1.3122 0.7763 0.8986 + 200SOL OW 598 0.446 0.239 1.024 0.0321 -0.2285 0.0174 + 200SOL HW1 599 0.426 0.256 0.928 -0.6769 0.6990 0.3210 + 200SOL HW2 600 0.440 0.325 1.075 1.7030 -0.4725 0.6645 + 201SOL OW 601 0.389 0.194 0.371 0.3108 -0.2167 0.5535 + 201SOL HW1 602 0.390 0.206 0.272 -0.3545 0.4874 0.6282 + 201SOL HW2 603 0.331 0.115 0.394 0.0047 -0.0376 0.4087 + 202SOL OW 604 0.672 1.424 0.815 -0.5655 0.8860 -0.1168 + 202SOL HW1 605 0.659 1.346 0.753 1.9136 -0.9085 1.5104 + 202SOL HW2 606 0.730 1.492 0.770 -0.6763 0.6517 -0.6213 + 203SOL OW 607 0.088 0.919 0.941 0.4703 0.3888 0.1022 + 203SOL HW1 608 0.118 0.832 0.980 -0.9147 -0.1690 -0.0698 + 203SOL HW2 609 -0.006 0.938 0.969 1.1561 2.4272 1.1431 + 204SOL OW 610 1.613 1.447 0.506 -0.2397 0.1224 -0.4911 + 204SOL HW1 611 1.574 1.455 0.414 -0.6147 -2.1473 -0.5397 + 204SOL HW2 612 1.539 1.443 0.573 0.0323 3.0606 0.0867 + 205SOL OW 613 1.801 1.172 1.523 -0.1389 0.0380 0.7452 + 205SOL HW1 614 1.813 1.262 1.566 -0.0595 0.0259 0.7478 + 205SOL HW2 615 1.830 1.176 1.427 -1.0958 0.2748 0.4670 + 206SOL OW 616 1.671 1.161 0.622 0.0381 -0.1968 -0.8982 + 206SOL HW1 617 1.659 1.062 0.624 1.0081 -0.2945 0.2200 + 206SOL HW2 618 1.665 1.194 0.528 -3.4793 -0.9138 -0.9865 + 207SOL OW 619 0.744 0.684 1.371 -0.4972 -0.4176 0.1462 + 207SOL HW1 620 0.819 0.647 1.316 -0.8700 -0.5741 -0.2655 + 207SOL HW2 621 0.664 0.697 1.313 -0.0811 1.9892 0.0593 + 208SOL OW 622 0.821 0.317 1.194 0.4536 0.4539 -0.3308 + 208SOL HW1 623 0.766 0.361 1.123 1.4276 0.6847 -0.9606 + 208SOL HW2 624 0.768 0.311 1.279 -0.1401 1.6828 -0.6050 + 209SOL OW 625 1.664 1.037 1.689 -0.3971 0.4743 0.3950 + 209SOL HW1 626 1.571 1.024 1.655 -0.4077 -0.2767 0.7076 + 209SOL HW2 627 1.711 1.105 1.632 -0.9022 0.3384 -0.1894 + 210SOL OW 628 1.819 0.231 0.807 -0.1924 0.5243 -0.1692 + 210SOL HW1 629 1.852 0.144 0.844 1.0633 0.7808 -0.6607 + 210SOL HW2 630 1.720 0.239 0.823 0.0839 0.0674 2.0047 + 211SOL OW 631 0.979 1.242 0.144 -0.2018 0.2018 -0.0354 + 211SOL HW1 632 0.938 1.316 0.090 -0.6232 -0.6929 -0.9633 + 211SOL HW2 633 0.946 1.247 0.238 -0.1197 1.2714 -0.0561 + 212SOL OW 634 0.778 0.948 0.748 0.5845 0.0149 -0.7815 + 212SOL HW1 635 0.818 1.006 0.676 -0.1841 1.1423 -0.3163 + 212SOL HW2 636 0.695 0.991 0.783 1.4375 -0.0808 1.4255 + 213SOL OW 637 1.814 1.673 1.613 -0.0991 0.5855 0.0909 + 213SOL HW1 638 1.826 1.683 1.712 0.1001 -0.7483 0.2122 + 213SOL HW2 639 1.873 1.599 1.580 -0.2204 0.9765 -1.0148 + 214SOL OW 640 0.068 1.175 1.260 0.2612 0.5460 0.5693 + 214SOL HW1 641 0.147 1.235 1.273 0.1725 0.8319 -0.1693 + 214SOL HW2 642 0.100 1.081 1.245 0.4518 0.6382 0.3995 + 215SOL OW 643 1.089 0.245 0.891 -0.1119 0.5785 0.4751 + 215SOL HW1 644 0.994 0.267 0.866 -0.3021 -0.0338 0.6459 + 215SOL HW2 645 1.099 0.146 0.898 0.6144 0.6299 0.1871 + 216SOL OW 646 1.135 1.550 0.658 0.1441 0.6409 -0.1721 + 216SOL HW1 647 1.078 1.522 0.736 0.3615 1.9482 0.4795 + 216SOL HW2 648 1.131 1.480 0.587 0.5499 -0.9515 1.3195 + 1.86060 1.86060 1.86060 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.top b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.top new file mode 100644 index 00000000..132cf50f --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.top @@ -0,0 +1,16 @@ +; +; +; Topology file for spce water +; +; +; +#include "oplsaa.ff/forcefield.itp" + +#include "oplsaa.ff/spce.itp" + +[ system ] +spce water + +[ molecules ] +SOL 216 + diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.tpr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.tpr new file mode 100644 index 00000000..cd0281cb Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.tpr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.trr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.trr new file mode 100644 index 00000000..1e71fbe0 Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/water.trr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/commands.sh b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/commands.sh new file mode 100755 index 00000000..2e31bc08 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/commands.sh @@ -0,0 +1,3 @@ +gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +gmx mdrun -s water.tpr -o water.trr diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/confout.gro new file mode 100644 index 00000000..ace3067e --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/confout.gro @@ -0,0 +1,651 @@ +spce water + 648 + 1SOL OW 1 0.427 0.087 1.634 0.0543 0.4447 -0.4346 + 1SOL HW1 2 0.353 0.154 1.635 0.8784 1.3949 -1.3017 + 1SOL HW2 3 0.393 0.000 1.598 -0.2872 1.3123 -2.2768 + 2SOL OW 4 0.366 0.991 0.648 0.5327 0.5425 -0.2172 + 2SOL HW1 5 0.377 0.913 0.585 -0.4094 -0.7034 1.1180 + 2SOL HW2 6 0.275 1.030 0.635 0.4064 0.3979 0.2345 + 3SOL OW 7 1.293 1.628 1.682 0.0822 0.3145 -0.1976 + 3SOL HW1 8 1.334 1.697 1.742 0.2048 -0.5586 0.7413 + 3SOL HW2 9 1.364 1.565 1.651 -0.1696 0.1180 -0.3762 + 4SOL OW 10 0.922 1.027 1.588 -0.0536 0.0223 0.6984 + 4SOL HW1 11 0.948 1.121 1.567 -0.6046 0.3474 1.4722 + 4SOL HW2 12 0.939 1.008 1.684 0.9957 -0.9842 0.3296 + 5SOL OW 13 0.871 1.326 0.395 -0.0959 -0.0153 -0.2603 + 5SOL HW1 14 0.954 1.367 0.432 -0.1428 -0.2136 0.0629 + 5SOL HW2 15 0.792 1.381 0.422 -0.2124 -0.6132 0.6170 + 6SOL OW 16 0.300 0.863 0.124 -0.1782 -0.4498 -0.1186 + 6SOL HW1 17 0.252 0.910 0.050 0.1891 1.7572 1.0184 + 6SOL HW2 18 0.299 0.920 0.206 0.2240 -2.4681 1.3236 + 7SOL OW 19 1.514 1.574 0.937 0.7431 0.0882 0.1220 + 7SOL HW1 20 1.575 1.495 0.938 0.5844 -0.0321 0.7093 + 7SOL HW2 21 1.442 1.562 1.006 -0.3585 -0.0884 -1.0279 + 8SOL OW 22 1.705 1.514 1.173 -0.2828 -0.1839 -0.3424 + 8SOL HW1 23 1.787 1.568 1.156 0.7519 -1.1420 1.5422 + 8SOL HW2 24 1.625 1.574 1.176 0.6120 0.9994 -0.1489 + 9SOL OW 25 1.346 0.399 0.374 -0.1956 0.3329 -0.3109 + 9SOL HW1 26 1.268 0.404 0.436 0.2693 -0.9197 0.3733 + 9SOL HW2 27 1.333 0.324 0.309 1.0778 -0.7844 0.6968 + 10SOL OW 28 1.416 0.982 1.613 -0.0594 0.3551 -0.1693 + 10SOL HW1 29 1.364 0.897 1.616 0.1658 0.1919 -0.7813 + 10SOL HW2 30 1.381 1.040 1.539 -0.6814 1.1062 0.6940 + 11SOL OW 31 0.579 1.437 1.073 -0.5008 -0.0920 -0.1331 + 11SOL HW1 32 0.643 1.498 1.120 0.5643 -0.8928 -0.4956 + 11SOL HW2 33 0.587 1.451 0.974 -1.0194 -0.0679 -0.1709 + 12SOL OW 34 0.427 0.541 0.668 0.3761 0.0072 0.1072 + 12SOL HW1 35 0.375 0.512 0.588 -1.1699 0.7092 0.8447 + 12SOL HW2 36 0.376 0.611 0.718 1.3551 -0.3761 1.6812 + 13SOL OW 37 1.496 0.946 1.174 0.0389 0.2811 -0.0905 + 13SOL HW1 38 1.555 0.868 1.153 3.1521 2.1433 1.3849 + 13SOL HW2 39 1.463 0.987 1.089 -0.1621 -1.5627 -0.9099 + 14SOL OW 40 1.416 1.196 0.728 -0.0095 -0.1319 0.4257 + 14SOL HW1 41 1.404 1.294 0.712 -0.3317 -0.0774 0.9771 + 14SOL HW2 42 1.482 1.159 0.663 -0.7353 0.2298 -0.5203 + 15SOL OW 43 0.619 0.002 0.834 -0.2568 -0.1233 -0.0013 + 15SOL HW1 44 0.574 -0.005 0.923 0.9074 1.7578 0.7678 + 15SOL HW2 45 0.569 0.067 0.776 0.3749 0.5215 0.1719 + 16SOL OW 46 1.846 0.346 0.269 -0.1465 0.4383 -0.2924 + 16SOL HW1 47 1.761 0.394 0.293 1.4008 3.2561 -0.2424 + 16SOL HW2 48 1.885 0.305 0.351 0.2965 2.0892 0.3494 + 17SOL OW 49 0.693 0.116 1.701 -0.1783 0.3285 0.5490 + 17SOL HW1 50 0.693 0.124 1.800 0.3709 0.6207 0.5308 + 17SOL HW2 51 0.599 0.117 1.667 -0.3827 -0.3026 1.1026 + 18SOL OW 52 0.456 1.027 1.253 0.5025 0.9371 -0.1716 + 18SOL HW1 53 0.481 1.104 1.311 -1.5811 3.2845 -2.2531 + 18SOL HW2 54 0.376 0.981 1.291 0.6890 0.8712 0.1457 + 19SOL OW 55 1.527 1.386 1.708 -0.2734 0.2399 -0.6448 + 19SOL HW1 56 1.602 1.420 1.765 -1.7610 0.7916 1.0299 + 19SOL HW2 57 1.499 1.295 1.740 -3.1521 1.8025 1.6149 + 20SOL OW 58 1.006 0.850 1.021 0.6892 0.0788 -0.1645 + 20SOL HW1 59 0.985 0.762 1.063 0.1564 0.1058 -0.3671 + 20SOL HW2 60 0.997 0.843 0.921 0.9299 0.2850 -0.2013 + 21SOL OW 61 0.847 0.985 0.318 0.2085 0.1430 0.0811 + 21SOL HW1 62 0.778 1.046 0.280 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FAIRmat-AreaC2-Rudzinski pid: 385680 rank ID: 0 number of ranks: 1 + :-) GROMACS - gmx mdrun, 2018.6 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra + Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru + Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus + Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl + Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola + Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov + Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2017, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2018.6 +Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/integrators_1frame +Command line: + gmx mdrun -s water.tpr -o water.trr + +GROMACS version: 2018.6 +Precision: single +Memory model: 64 bit +MPI library: thread_mpi +OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) +GPU support: OpenCL +SIMD instructions: SSE2 +FFT library: fftw-3.3.8-sse2-avx +RDTSCP usage: disabled +TNG support: enabled +Hwloc support: hwloc-1.11.9 +Tracing support: disabled +Built on: 2019-05-12 20:18:02 +Built by: root@default-0e84dd72-7298-44a4-a670-e10728e370dd [CMAKE] +Build OS/arch: Linux 4.4.0-96-generic x86_64 +Build CPU vendor: Unknown +Build CPU brand: Unknown +Build CPU family: 0 Model: 0 Stepping: 0 +Build CPU features: Unknown +C compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc GNU 7.3.0 +C compiler flags: -msse2 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +C++ compiler: /opt/conda/conda-bld/gromacs_1557692095347/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ GNU 7.3.0 +C++ compiler flags: -msse2 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jfrudzinski/miniconda3/envs/martignac_2/include -fdebug-prefix-map=/opt/conda/conda-bld/gromacs_1557692095347/work=/usr/local/src/conda/gromacs-2018.6 -fdebug-prefix-map=/home/jfrudzinski/miniconda3/envs/martignac_2=/usr/local/src/conda-prefix -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast +OpenCL include dir: /home/jfrudzinski/miniconda3/envs/martignac_2/include +OpenCL library: /home/jfrudzinski/miniconda3/envs/martignac_2/lib/libOpenCL.so +OpenCL version: 2.0 + +NOTE: Detection of GPUs failed. The API reported: + GROMACS cannot run tasks on a GPU. + +Running on 1 node with total 4 cores, 8 logical cores, 0 compatible GPUs +Hardware detected: + CPU info: + Vendor: Intel + Brand: 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz + Family: 6 Model: 140 Stepping: 1 + Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic + Number of AVX-512 FMA units: Cannot run AVX-512 detection - assuming 2 + Hardware topology: Full, with devices + Sockets, cores, and logical processors: + Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] + Numa nodes: + Node 0 (16138244096 bytes mem): 0 1 2 3 4 5 6 7 + Latency: + 0 + 0 1.00 + Caches: + L1: 49152 bytes, linesize 64 bytes, assoc. 12, shared 2 ways + L2: 1310720 bytes, linesize 64 bytes, assoc. 20, shared 2 ways + L3: 12582912 bytes, linesize 64 bytes, assoc. 12, shared 8 ways + PCI devices: + 0000:00:02.0 Id: 8086:9a49 Class: 0x0300 Numa: 0 + 0000:00:0e.0 Id: 8086:9a0b Class: 0x0104 Numa: 0 + 0000:00:14.3 Id: 8086:a0f0 Class: 0x0280 Numa: 0 + 0000:00:1f.6 Id: 8086:15fb Class: 0x0200 Numa: 0 + +Highest SIMD level requested by all nodes in run: AVX_512 +SIMD instructions selected at compile time: SSE2 +This program was compiled for different hardware than you are running on, +which could influence performance. + +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. +Lindahl +GROMACS: High performance molecular simulations through multi-level +parallelism from laptops to supercomputers +SoftwareX 1 (2015) pp. 19-25 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl +Tackling Exascale Software Challenges in Molecular Dynamics Simulations with +GROMACS +In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. +Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl +GROMACS 4.5: a high-throughput and highly parallel open source molecular +simulation toolkit +Bioinformatics 29 (2013) pp. 845-54 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl +GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable +molecular simulation +J. Chem. Theory Comput. 4 (2008) pp. 435-447 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. +Berendsen +GROMACS: Fast, Flexible and Free +J. Comp. Chem. 26 (2005) pp. 1701-1719 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +E. Lindahl and B. Hess and D. van der Spoel +GROMACS 3.0: A package for molecular simulation and trajectory analysis +J. Mol. Mod. 7 (2001) pp. 306-317 +-------- -------- --- Thank You --- -------- -------- + + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +H. J. C. Berendsen, D. van der Spoel and R. van Drunen +GROMACS: A message-passing parallel molecular dynamics implementation +Comp. Phys. Comm. 91 (1995) pp. 43-56 +-------- -------- --- Thank You --- -------- -------- + +Input Parameters: + integrator = sd + tinit = 0 + dt = 0.001 + nsteps = 1 + init-step = 0 + simulation-part = 1 + comm-mode = Linear + nstcomm = 1 + bd-fric = 0 + ld-seed = 651126194 + emtol = 10 + emstep = 0.01 + niter = 20 + fcstep = 0 + nstcgsteep = 1000 + nbfgscorr = 10 + rtpi = 0.05 + nstxout = 1 + nstvout = 1 + nstfout = 1 + nstlog = 1 + nstcalcenergy = 1 + nstenergy = 1 + nstxout-compressed = 0 + compressed-x-precision = 1000 + cutoff-scheme = Verlet + nstlist = 1 + ns-type = Grid + pbc = xyz + periodic-molecules = false + verlet-buffer-tolerance = 0.005 + rlist = 0.9 + coulombtype = PME + coulomb-modifier = Potential-shift + rcoulomb-switch = 0 + rcoulomb = 0.9 + epsilon-r = 1 + epsilon-rf = inf + vdw-type = Cut-off + vdw-modifier = Potential-shift + rvdw-switch = 0 + rvdw = 0.9 + DispCorr = EnerPres + table-extension = 1 + fourierspacing = 0.08 + fourier-nx = 24 + fourier-ny = 24 + fourier-nz = 24 + pme-order = 6 + ewald-rtol = 1e-06 + ewald-rtol-lj = 0.001 + lj-pme-comb-rule = Geometric + ewald-geometry = 0 + epsilon-surface = 0 + implicit-solvent = No + gb-algorithm = Still + nstgbradii = 1 + rgbradii = 1 + gb-epsilon-solvent = 80 + gb-saltconc = 0 + gb-obc-alpha = 1 + gb-obc-beta = 0.8 + gb-obc-gamma = 4.85 + gb-dielectric-offset = 0.009 + sa-algorithm = Ace-approximation + sa-surface-tension = 2.05016 + tcoupl = No + nsttcouple = -1 + nh-chain-length = 0 + print-nose-hoover-chain-variables = false + pcoupl = No + pcoupltype = Isotropic + nstpcouple = -1 + tau-p = 1 + compressibility (3x3): + compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p (3x3): + ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + refcoord-scaling = No + posres-com (3): + posres-com[0]= 0.00000e+00 + posres-com[1]= 0.00000e+00 + posres-com[2]= 0.00000e+00 + posres-comB (3): + posres-comB[0]= 0.00000e+00 + posres-comB[1]= 0.00000e+00 + posres-comB[2]= 0.00000e+00 + QMMM = false + QMconstraints = 0 + QMMMscheme = 0 + MMChargeScaleFactor = 1 +qm-opts: + ngQM = 0 + constraint-algorithm = Lincs + continuation = false + Shake-SOR = false + shake-tol = 0.0001 + lincs-order = 4 + lincs-iter = 1 + lincs-warnangle = 30 + nwall = 0 + wall-type = 9-3 + wall-r-linpot = -1 + wall-atomtype[0] = -1 + wall-atomtype[1] = -1 + wall-density[0] = 0 + wall-density[1] = 0 + wall-ewald-zfac = 3 + pull = false + awh = false + rotation = false + interactiveMD = false + disre = No + disre-weighting = Conservative + disre-mixed = false + dr-fc = 1000 + dr-tau = 0 + nstdisreout = 100 + orire-fc = 0 + orire-tau = 0 + nstorireout = 100 + free-energy = no + cos-acceleration = 0 + deform (3x3): + deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} + simulated-tempering = false + swapcoords = no + userint1 = 0 + userint2 = 0 + userint3 = 0 + userint4 = 0 + userreal1 = 0 + userreal2 = 0 + userreal3 = 0 + userreal4 = 0 + applied-forces: + electric-field: + x: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + y: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 + z: + E0 = 0 + omega = 0 + t0 = 0 + sigma = 0 +grpopts: + nrdf: 1293 + ref-t: 298 + tau-t: 0.5 +annealing: No +annealing-npoints: 0 + acc: 0 0 0 + nfreeze: N N N + energygrp-flags[ 0]: 0 + + +Using 1 MPI thread +Using 8 OpenMP threads + +Pinning threads with an auto-selected logical core stride of 1 +System total charge: 0.000 +Will do PME sum in reciprocal space for electrostatic interactions. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen +A smooth particle mesh Ewald method +J. Chem. Phys. 103 (1995) pp. 8577-8592 +-------- -------- --- Thank You --- -------- -------- + +Using a Gaussian width (1/beta) of 0.260197 nm for Ewald +Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-06 +Initialized non-bonded Ewald correction tables, spacing: 8.41e-04 size: 1071 + +Long Range LJ corr.: 2.9078e-04 +Generated table with 950 data points for Ewald. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ6. +Tabscale = 500 points/nm +Generated table with 950 data points for LJ12. +Tabscale = 500 points/nm + +Using SIMD 4x4 nonbonded short-range kernels + +Using a 4x4 pair-list setup: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm +At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: + updated every 1 steps, buffer 0.000 nm, rlist 0.900 nm + +Using geometric Lennard-Jones combination rule + +Removing pbc first time + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +S. Miyamoto and P. A. Kollman +SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid +Water Models +J. Comp. Chem. 13 (1992) pp. 952-962 +-------- -------- --- Thank You --- -------- -------- + + +Intra-simulation communication will occur every 1 steps. +Center of mass motion removal mode is Linear +We have the following groups for center of mass motion removal: + 0: rest + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C. +Berendsen +Efficient Algorithms for Langevin and DPD Dynamics +J. Chem. Theory Comput. 8 (2012) pp. 3637--3649 +-------- -------- --- Thank You --- -------- -------- + +There are: 648 Atoms + +Constraining the starting coordinates (step 0) + +Constraining the coordinates at t0-dt (step 0) +RMS relative constraint deviation after constraining: 0.00e+00 +Initial temperature: 299.045 K + +Started mdrun on rank 0 Wed Jan 3 14:56:26 2024 + Step Time + 0 0.00000 + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.98181e+03 -1.08747e+02 -1.21912e+04 1.28385e+02 -1.01898e+04 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.61768e+03 -8.57208e+03 3.00948e+02 -2.80811e+02 -5.11119e+02 + + Step Time + 1 0.00100 + +Writing checkpoint, step 1 at Wed Jan 3 14:56:26 2024 + + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97775e+03 -1.08747e+02 -1.22025e+04 1.24428e+02 -1.02090e+04 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.63695e+03 -8.57210e+03 3.04532e+02 -2.80811e+02 -6.09001e+02 + + <====== ############### ==> + <==== A V E R A G E S ====> + <== ############### ======> + + Statistics over 2 steps using 2 frames + + Energies (kJ/mol) + LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential + 1.97978e+03 -1.08747e+02 -1.21968e+04 1.26407e+02 -1.01994e+04 + Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) + 1.62732e+03 -8.57209e+03 3.02740e+02 -2.80811e+02 -5.60060e+02 + + Total Virial (kJ/mol) + 6.69609e+02 1.15288e+02 1.45554e+02 + 1.15346e+02 5.78633e+02 -7.83009e+00 + 1.45903e+02 -7.10872e+00 7.04938e+02 + + Pressure (bar) + -7.60101e+02 -5.11688e+02 -6.03046e+02 + -5.11985e+02 -3.72282e+02 8.20121e+01 + -6.04846e+02 7.82927e+01 -5.47797e+02 + + + M E G A - F L O P S A C C O U N T I N G + + NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels + RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table + W3=SPC/TIP3p W4=TIP4p (single or pairs) + V&F=Potential and force V=Potential only F=Force only + + Computing: M-Number M-Flops % Flops +----------------------------------------------------------------------------- + Pair Search distance check 0.304438 2.740 8.5 + NxN QSTab Elec. + LJ [V&F] 0.205984 12.153 37.8 + NxN QSTab Elec. [V&F] 0.198208 8.127 25.3 + Calc Weights 0.003888 0.140 0.4 + Spread Q Bspline 0.279936 0.560 1.7 + Gather F Bspline 0.279936 1.680 5.2 + 3D-FFT 0.760588 6.085 18.9 + Solve PME 0.001152 0.074 0.2 + Shift-X 0.001296 0.008 0.0 + Virial 0.001386 0.025 0.1 + Update 0.001296 0.040 0.1 + Stop-CM 0.001944 0.019 0.1 + Calc-Ekin 0.001944 0.052 0.2 + Constraint-V 0.003240 0.026 0.1 + Constraint-Vir 0.001296 0.031 0.1 + Settle 0.001296 0.419 1.3 +----------------------------------------------------------------------------- + Total 32.178 100.0 +----------------------------------------------------------------------------- + + + R E A L C Y C L E A N D T I M E A C C O U N T I N G + +On 1 MPI rank, each using 8 OpenMP threads + + Computing: Num Num Call Wall time Giga-Cycles + Ranks Threads Count (s) total sum % +----------------------------------------------------------------------------- + Neighbor search 1 8 2 0.001 0.014 3.1 + Force 1 8 2 0.001 0.012 2.7 + PME mesh 1 8 2 0.000 0.005 1.2 + NB X/F buffer ops. 1 8 2 0.000 0.000 0.0 + Write traj. 1 8 2 0.017 0.252 55.1 + Update 1 8 4 0.011 0.159 34.8 + Constraints 1 8 4 0.000 0.002 0.5 + Rest 0.001 0.012 2.5 +----------------------------------------------------------------------------- + Total 0.032 0.457 100.0 +----------------------------------------------------------------------------- + Breakdown of PME mesh computation +----------------------------------------------------------------------------- + PME spread 1 8 2 0.000 0.002 0.5 + PME gather 1 8 2 0.000 0.002 0.3 + PME 3D-FFT 1 8 4 0.000 0.001 0.3 + PME solve Elec 1 8 2 0.000 0.000 0.1 +----------------------------------------------------------------------------- + + Core t (s) Wall t (s) (%) + Time: 0.253 0.032 800.0 + (ns/day) (hour/ns) +Performance: 5.461 4.395 +Finished mdrun on rank 0 Wed Jan 3 14:56:26 2024 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/mdout.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/mdout.mdp new file mode 100644 index 00000000..ff10e642 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/mdout.mdp @@ -0,0 +1,353 @@ +; +; File 'mdout.mdp' was generated +; By user: jfrudzinski (1000) +; On host: FAIRmat-AreaC2-Rudzinski +; At date: Wed Jan 3 14:54:36 2024 +; +; Created by: +; :-) GROMACS - gmx grompp, 2018.6 (-: +; +; Executable: /home/jfrudzinski/miniconda3/envs/martignac_2/bin/gmx +; Data prefix: /home/jfrudzinski/miniconda3/envs/martignac_2 +; Working dir: /home/jfrudzinski/work/DEV_Examples/GRO_DEV/MD_Overview/Water/integrators_1frame +; Command line: +; gmx grompp -f water.298.mdp -c water.confout.gro -p water.top -o water.tpr + +; VARIOUS PREPROCESSING OPTIONS +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/roe +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ +; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) +define = + +; RUN CONTROL PARAMETERS +integrator = sd +; Start time and timestep in ps +tinit = 0.0 +dt = 0.001 +nsteps = 1 +; For exact run continuation or redoing part of a run +init-step = 0 +; Part index is updated automatically on checkpointing (keeps files separate) +simulation-part = 1 +; mode for center of mass motion removal +comm-mode = linear +; number of steps for center of mass motion removal +nstcomm = 1 +; group(s) for center of mass motion removal +comm-grps = + +; LANGEVIN DYNAMICS OPTIONS +; Friction coefficient (amu/ps) and random seed +bd-fric = 0 +ld-seed = -1 + +; ENERGY MINIMIZATION OPTIONS +; Force tolerance and initial step-size +emtol = 10 +emstep = 0.01 +; Max number of iterations in relax-shells +niter = 20 +; Step size (ps^2) for minimization of flexible constraints +fcstep = 0 +; Frequency of steepest descents steps when doing CG +nstcgsteep = 1000 +nbfgscorr = 10 + +; TEST PARTICLE INSERTION OPTIONS +rtpi = 0.05 + +; OUTPUT CONTROL OPTIONS +; Output frequency for coords (x), velocities (v) and forces (f) +nstxout = 1 +nstvout = 1 +nstfout = 1 +; Output frequency for energies to log file and energy file +nstlog = 1 +nstcalcenergy = 100 +nstenergy = 1 +; Output frequency and precision for .xtc file +nstxout-compressed = 0 +compressed-x-precision = 1000 +; This selects the subset of atoms for the compressed +; trajectory file. You can select multiple groups. By +; default, all atoms will be written. +compressed-x-grps = +; Selection of energy groups +energygrps = System + +; NEIGHBORSEARCHING PARAMETERS +; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) +cutoff-scheme = Verlet +; nblist update frequency +nstlist = 1 +; ns algorithm (simple or grid) +ns_type = grid +; Periodic boundary conditions: xyz, no, xy +pbc = xyz +periodic-molecules = no +; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, +; a value of -1 means: use rlist +verlet-buffer-tolerance = 0.005 +; nblist cut-off +rlist = 0.9 +; long-range cut-off for switched potentials + +; OPTIONS FOR ELECTROSTATICS AND VDW +; Method for doing electrostatics +coulombtype = PME +coulomb-modifier = Potential-shift-Verlet +rcoulomb-switch = 0 +rcoulomb = 0.9 +; Relative dielectric constant for the medium and the reaction field +epsilon-r = 1 +epsilon-rf = 0 +; Method for doing Van der Waals +vdwtype = cutoff +vdw-modifier = Potential-shift-Verlet +; cut-off lengths +rvdw-switch = 0 +rvdw = 0.9 +; Apply long range dispersion corrections for Energy and Pressure +DispCorr = EnerPres +; Extension of the potential lookup tables beyond the cut-off +table-extension = 1 +; Separate tables between energy group pairs +energygrp-table = +; Spacing for the PME/PPPM FFT grid +fourierspacing = 0.08 +; FFT grid size, when a value is 0 fourierspacing will be used +fourier-nx = 0 +fourier-ny = 0 +fourier-nz = 0 +; EWALD/PME/PPPM parameters +pme_order = 6 +ewald_rtol = 1e-06 +ewald-rtol-lj = 0.001 +lj-pme-comb-rule = Geometric +ewald-geometry = 3d +epsilon-surface = 0 + +; IMPLICIT SOLVENT ALGORITHM +implicit-solvent = No + +; GENERALIZED BORN ELECTROSTATICS +; Algorithm for calculating Born radii +gb-algorithm = Still +; Frequency of calculating the Born radii inside rlist +nstgbradii = 1 +; Cutoff for Born radii calculation; the contribution from atoms +; between rlist and rgbradii is updated every nstlist steps +rgbradii = 1 +; Dielectric coefficient of the implicit solvent +gb-epsilon-solvent = 80 +; Salt concentration in M for Generalized Born models +gb-saltconc = 0 +; Scaling factors used in the OBC GB model. Default values are OBC(II) +gb-obc-alpha = 1 +gb-obc-beta = 0.8 +gb-obc-gamma = 4.85 +gb-dielectric-offset = 0.009 +sa-algorithm = Ace-approximation +; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA +; The value -1 will set default value for Still/HCT/OBC GB-models. +sa-surface-tension = -1 + +; OPTIONS FOR WEAK COUPLING ALGORITHMS +; Temperature coupling +tcoupl = No +nsttcouple = -1 +nh-chain-length = 10 +print-nose-hoover-chain-variables = no +; Groups to couple separately +tc_grps = System +; Time constant (ps) and reference temperature (K) +tau_t = 0.5 +ref_t = 298 +; pressure coupling +pcoupl = No +pcoupltype = Isotropic +nstpcouple = -1 +; Time constant (ps), compressibility (1/bar) and reference P (bar) +tau-p = 1 +compressibility = +ref-p = +; Scaling of reference coordinates, No, All or COM +refcoord-scaling = No + +; OPTIONS FOR QMMM calculations +QMMM = no +; Groups treated Quantum Mechanically +QMMM-grps = +; QM method +QMmethod = +; QMMM scheme +QMMMscheme = normal +; QM basisset +QMbasis = +; QM charge +QMcharge = +; QM multiplicity +QMmult = +; Surface Hopping +SH = +; CAS space options +CASorbitals = +CASelectrons = +SAon = +SAoff = +SAsteps = +; Scale factor for MM charges +MMChargeScaleFactor = 1 + +; SIMULATED ANNEALING +; Type of annealing for each temperature group (no/single/periodic) +annealing = +; Number of time points to use for specifying annealing in each group +annealing-npoints = +; List of times at the annealing points for each group +annealing-time = +; Temp. at each annealing point, for each group. +annealing-temp = + +; GENERATE VELOCITIES FOR STARTUP RUN +gen_vel = yes +gen_temp = 298 +gen_seed = 173529 + +; OPTIONS FOR BONDS +constraints = none +; Type of constraint algorithm +constraint-algorithm = Lincs +; Do not constrain the start configuration +continuation = no +; Use successive overrelaxation to reduce the number of shake iterations +Shake-SOR = no +; Relative tolerance of shake +shake-tol = 0.0001 +; Highest order in the expansion of the constraint coupling matrix +lincs-order = 4 +; Number of iterations in the final step of LINCS. 1 is fine for +; normal simulations, but use 2 to conserve energy in NVE runs. +; For energy minimization with constraints it should be 4 to 8. +lincs-iter = 1 +; Lincs will write a warning to the stderr if in one step a bond +; rotates over more degrees than +lincs-warnangle = 30 +; Convert harmonic bonds to morse potentials +morse = no + +; ENERGY GROUP EXCLUSIONS +; Pairs of energy groups for which all non-bonded interactions are excluded +energygrp-excl = + +; WALLS +; Number of walls, type, atom types, densities and box-z scale factor for Ewald +nwall = 0 +wall-type = 9-3 +wall-r-linpot = -1 +wall-atomtype = +wall-density = +wall-ewald-zfac = 3 + +; COM PULLING +pull = no + +; AWH biasing +awh = no + +; ENFORCED ROTATION +; Enforced rotation: No or Yes +rotation = no + +; Group to display and/or manipulate in interactive MD session +IMD-group = + +; NMR refinement stuff +; Distance restraints type: No, Simple or Ensemble +disre = No +; Force weighting of pairs in one distance restraint: Conservative or Equal +disre-weighting = Conservative +; Use sqrt of the time averaged times the instantaneous violation +disre-mixed = no +disre-fc = 1000 +disre-tau = 0 +; Output frequency for pair distances to energy file +nstdisreout = 100 +; Orientation restraints: No or Yes +orire = no +; Orientation restraints force constant and tau for time averaging +orire-fc = 0 +orire-tau = 0 +orire-fitgrp = +; Output frequency for trace(SD) and S to energy file +nstorireout = 100 + +; Free energy variables +free-energy = no +couple-moltype = +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q +couple-intramol = no +init-lambda = -1 +init-lambda-state = -1 +delta-lambda = 0 +nstdhdl = 50 +fep-lambdas = +mass-lambdas = +coul-lambdas = +vdw-lambdas = +bonded-lambdas = +restraint-lambdas = +temperature-lambdas = +calc-lambda-neighbors = 1 +init-lambda-weights = +dhdl-print-energy = no +sc-alpha = 0 +sc-power = 1 +sc-r-power = 6 +sc-sigma = 0.3 +sc-coul = no +separate-dhdl-file = yes +dhdl-derivatives = yes +dh_hist_size = 0 +dh_hist_spacing = 0.1 + +; Non-equilibrium MD stuff +acc-grps = +accelerate = +freezegrps = +freezedim = +cos-acceleration = 0 +deform = + +; simulated tempering variables +simulated-tempering = no +simulated-tempering-scaling = geometric +sim-temp-low = 300 +sim-temp-high = 300 + +; Ion/water position swapping for computational electrophysiology setups +; Swap positions along direction: no, X, Y, Z +swapcoords = no +adress = no + +; User defined thingies +user1-grps = +user2-grps = +userint1 = 0 +userint2 = 0 +userint3 = 0 +userint4 = 0 +userreal1 = 0 +userreal2 = 0 +userreal3 = 0 +userreal4 = 0 +; Electric fields +; Format for electric-field-x, etc. is: four real variables: +; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), +; and sigma (ps) width of the pulse. Omega = 0 means static field, +; sigma = 0 means no pulse, leaving the field to be a cosine function. +electric-field-x = 0 0 0 0 +electric-field-y = 0 0 0 0 +electric-field-z = 0 0 0 0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/state.cpt b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/state.cpt new file mode 100644 index 00000000..b407089f Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/state.cpt differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.298.mdp b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.298.mdp new file mode 100644 index 00000000..19898243 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.298.mdp @@ -0,0 +1,52 @@ +; Preprocessing +include = -I/gpfs/work/jfr148/pkg/gromacs-4.0.7/share/top/ + +; Run Control +integrator = sd +tinit = 0.0 +dt = 0.001 ; 1.0 fs +nsteps = 1 ; 20 ns +nstcomm = 1 ; no. steps between removing com motion +comm-mode = linear ; remove com translation + +; Output Control +nstxout = 1 ; no. steps between printing coords to trr file => 1ps +nstvout = 1 ; no. steps between printing veloc to trr file +nstfout = 1 ; no. steps between printing forces to trr file => 1ps +nstlog = 1 ; no. steps between printing energy to log file => 1ps +nstenergy = 1 ; no. steps between printing energy to edr file => 1ps +nstxtcout = 0 ; no. stpes between printing coords to xtc file +energygrps = System ; groups for writing energy file + +; Neighbor searching +nstlist = 1 ; update neighbor list every step +ns_type = grid ; check neighbor list using grid +rlist = 0.9 ; cutoff distance (nm) for short-range neighbor list + +; Electrostatics and VdW +coulombtype = PME ; fast particle-mesh ewald electrostatics +rcoulomb = 0.9 ; distance for the Coulomb cut-off +vdwtype = cutoff ; truncated LJ interactions +rvdw = 0.9 ; distance for LJ cut-off +DispCorr = EnerPres ; apply long range disp. correct. for Energy/Pres +fourierspacing = 0.08 ; max grid spacing fr FFT grid in PME +pme_order = 6 ; interpolation order for PME +ewald_rtol = 1e-06 ; relative strength of direct potential at cutoff +optimize_fft = yes ; optimize fft_grids + +; Temperature Coupling +;tcoupl = nose-hoover ; nose-hoover for correct ensemble +tc_grps = System ; groups to couple separtly to temp. bath +tau_t = 0.5 ; time constant for coupling +ref_t = 298 ; ref. temperature for coupling + +; Velocity generation +gen_vel = yes ; generate velocities with Max. dist. +gen_temp = 298 ; temp. for Max. dist. +gen_seed = 173529 ; for random number generator + +; Pressure coupling +;pcoupl = Parrinello-Rahman +;tau-p = 5.0 +;compressibility = 7.4e-5 +;ref-p = 1.0 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.confout.gro b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.confout.gro new file mode 100644 index 00000000..0244d504 --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.confout.gro 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HW2 636 0.695 0.991 0.783 1.4375 -0.0808 1.4255 + 213SOL OW 637 1.814 1.673 1.613 -0.0991 0.5855 0.0909 + 213SOL HW1 638 1.826 1.683 1.712 0.1001 -0.7483 0.2122 + 213SOL HW2 639 1.873 1.599 1.580 -0.2204 0.9765 -1.0148 + 214SOL OW 640 0.068 1.175 1.260 0.2612 0.5460 0.5693 + 214SOL HW1 641 0.147 1.235 1.273 0.1725 0.8319 -0.1693 + 214SOL HW2 642 0.100 1.081 1.245 0.4518 0.6382 0.3995 + 215SOL OW 643 1.089 0.245 0.891 -0.1119 0.5785 0.4751 + 215SOL HW1 644 0.994 0.267 0.866 -0.3021 -0.0338 0.6459 + 215SOL HW2 645 1.099 0.146 0.898 0.6144 0.6299 0.1871 + 216SOL OW 646 1.135 1.550 0.658 0.1441 0.6409 -0.1721 + 216SOL HW1 647 1.078 1.522 0.736 0.3615 1.9482 0.4795 + 216SOL HW2 648 1.131 1.480 0.587 0.5499 -0.9515 1.3195 + 1.86060 1.86060 1.86060 diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.top b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.top new file mode 100644 index 00000000..132cf50f --- /dev/null +++ b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.top @@ -0,0 +1,16 @@ +; +; +; Topology file for spce water +; +; +; +#include "oplsaa.ff/forcefield.itp" + +#include "oplsaa.ff/spce.itp" + +[ system ] +spce water + +[ molecules ] +SOL 216 + diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.tpr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.tpr new file mode 100644 index 00000000..9557f76b Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.tpr differ diff --git a/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.trr b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.trr new file mode 100644 index 00000000..979cf4cd Binary files /dev/null and b/tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/water.trr differ diff --git a/tests/test_gromacsparser.py b/tests/test_gromacsparser.py index ea4f8400..5ef31e30 100644 --- a/tests/test_gromacsparser.py +++ b/tests/test_gromacsparser.py @@ -27,44 +27,61 @@ def approx(value, abs=0, rel=1e-6): return pytest.approx(value, abs=abs, rel=rel) -@pytest.fixture(scope='module') +@pytest.fixture(scope="module") def parser(): return GromacsParser() def test_md_verbose(parser): archive = EntryArchive() - parser.parse('tests/data/gromacs/fe_test/md.log', archive, None) + parser.parse("tests/data/gromacs/fe_test/md.log", archive, None) sec_run = archive.run[0] - assert sec_run.program.version == '5.1.4' + assert sec_run.program.version == "5.1.4" sec_control = sec_run.x_gromacs_section_control_parameters - assert sec_control.x_gromacs_inout_control_coulombtype == 'PME' + assert sec_control.x_gromacs_inout_control_coulombtype == "PME" assert np.shape(sec_control.x_gromacs_inout_control_deform) == (3, 3) sec_workflow = archive.workflow2 - assert sec_workflow.m_def.name == 'MolecularDynamics' + assert sec_workflow.m_def.name == "MolecularDynamics" sec_method = sec_workflow.method - assert sec_method.thermodynamic_ensemble == 'NPT' - assert sec_method.integrator_type == 'leap_frog' + assert sec_method.thermodynamic_ensemble == "NPT" + assert sec_method.integrator_type == "leap_frog" assert sec_method.integration_timestep.magnitude == 5e-16 - assert sec_method.integration_timestep.units == 'second' + assert sec_method.integration_timestep.units == "second" assert sec_method.n_steps == 20 assert sec_method.coordinate_save_frequency == 20 assert sec_method.thermodynamics_save_frequency == 5 - assert sec_method.thermostat_parameters[0].thermostat_type == 'berendsen' + assert sec_method.thermostat_parameters[0].thermostat_type == "berendsen" assert sec_method.thermostat_parameters[0].reference_temperature.magnitude == 298.0 - assert sec_method.thermostat_parameters[0].reference_temperature.units == 'kelvin' + assert sec_method.thermostat_parameters[0].reference_temperature.units == "kelvin" assert sec_method.thermostat_parameters[0].coupling_constant.magnitude == 5e-13 - assert sec_method.thermostat_parameters[0].coupling_constant.units == 'second' - assert sec_method.barostat_parameters[0].barostat_type == 'berendsen' - assert sec_method.barostat_parameters[0].coupling_type == 'isotropic' - assert np.all(sec_method.barostat_parameters[0].reference_pressure.magnitude == [[100000., 0., 0.], [0., 100000., 0.], [0., 0., 100000.]]) - assert sec_method.barostat_parameters[0].reference_pressure.units == 'pascal' - assert np.all(sec_method.barostat_parameters[0].coupling_constant.magnitude == [[1.e-12, 1.e-12, 1.e-12], [1.e-12, 1.e-12, 1.e-12], [1.e-12, 1.e-12, 1.e-12]]) - assert sec_method.barostat_parameters[0].coupling_constant.units == 'second' - assert np.all(sec_method.barostat_parameters[0].compressibility.magnitude == [[4.6e-10, 0.0e+00, 0.0e+00], [0.0e+00, 4.6e-10, 0.0e+00], [0.0e+00, 0.0e+00, 4.6e-10]]) - assert sec_method.barostat_parameters[0].compressibility.units == '1 / pascal' + assert sec_method.thermostat_parameters[0].coupling_constant.units == "second" + assert sec_method.barostat_parameters[0].barostat_type == "berendsen" + assert sec_method.barostat_parameters[0].coupling_type == "isotropic" + assert np.all( + sec_method.barostat_parameters[0].reference_pressure.magnitude + == [[100000.0, 0.0, 0.0], [0.0, 100000.0, 0.0], [0.0, 0.0, 100000.0]] + ) + assert sec_method.barostat_parameters[0].reference_pressure.units == "pascal" + assert np.all( + sec_method.barostat_parameters[0].coupling_constant.magnitude + == [ + [1.0e-12, 1.0e-12, 1.0e-12], + [1.0e-12, 1.0e-12, 1.0e-12], + [1.0e-12, 1.0e-12, 1.0e-12], + ] + ) + assert sec_method.barostat_parameters[0].coupling_constant.units == "second" + assert np.all( + sec_method.barostat_parameters[0].compressibility.magnitude + == [ + [4.6e-10, 0.0e00, 0.0e00], + [0.0e00, 4.6e-10, 0.0e00], + [0.0e00, 0.0e00, 4.6e-10], + ] + ) + assert sec_method.barostat_parameters[0].compressibility.units == "1 / pascal" sec_sccs = sec_run.calculation assert len(sec_sccs) == 5 @@ -73,25 +90,47 @@ def test_md_verbose(parser): assert sec_sccs[3].temperature.magnitude == approx(291.80401611328125) assert sec_sccs[2].volume.magnitude == approx(1.505580043792725e-26) assert sec_sccs[2].density.magnitude == approx(1007.9478759765625) - assert sec_sccs[2].enthalpy.magnitude == approx(-1.184108268425108e+31) + assert sec_sccs[2].enthalpy.magnitude == approx(-1.184108268425108e31) assert sec_sccs[2].virial_tensor[2][2].magnitude == approx(1.1367756347656254e-19) assert len(sec_sccs[1].x_gromacs_thermodynamics_contributions) == 5 - assert sec_sccs[1].x_gromacs_thermodynamics_contributions[2].kind == '#Surf*SurfTen' - assert sec_sccs[1].x_gromacs_thermodynamics_contributions[2].value == approx(2453.242431640625) + assert sec_sccs[1].x_gromacs_thermodynamics_contributions[2].kind == "#Surf*SurfTen" + assert sec_sccs[1].x_gromacs_thermodynamics_contributions[2].value == approx( + 2453.242431640625 + ) assert len(sec_sccs[4].energy.x_gromacs_energy_contributions) == 12 - assert sec_sccs[-2].energy.x_gromacs_energy_contributions[1].kind == 'G96Angle' - assert sec_sccs[-2].energy.x_gromacs_energy_contributions[1].value.magnitude == approx(9.90594089232063e+27) - assert sec_sccs[0].energy.total.value.magnitude == approx(-1.1863129365544755e+31) - assert sec_sccs[0].energy.electrostatic.value.magnitude == approx(-1.6677869795296e+31) - assert sec_sccs[0].energy.electrostatic.short_range.magnitude == approx(-1.5069901728906464e+31) - assert sec_sccs[0].energy.electrostatic.long_range.magnitude == approx(-1.6079680663895344e+30) - assert sec_sccs[-1].energy.van_der_waals.value.magnitude == approx(2.5995702480888255e+30) - assert sec_sccs[-1].energy.van_der_waals.short_range.magnitude == approx(2.675488981642447e+30) - assert sec_sccs[-1].energy.van_der_waals.long_range.magnitude == approx(-4.4191382265877185e+28) - assert sec_sccs[-1].energy.van_der_waals.correction.magnitude == approx(-3.172735128774431e+28) - assert sec_sccs[0].energy.pressure_volume_work.value.magnitude == approx(5.46058641332406e+26) - - assert sec_sccs[0].forces.total.value[5][2].magnitude == approx(-7.932968909721231e-10) + assert sec_sccs[-2].energy.x_gromacs_energy_contributions[1].kind == "G96Angle" + assert sec_sccs[-2].energy.x_gromacs_energy_contributions[ + 1 + ].value.magnitude == approx(9.90594089232063e27) + assert sec_sccs[0].energy.total.value.magnitude == approx(-1.1863129365544755e31) + assert sec_sccs[0].energy.electrostatic.value.magnitude == approx( + -1.6677869795296e31 + ) + assert sec_sccs[0].energy.electrostatic.short_range.magnitude == approx( + -1.5069901728906464e31 + ) + assert sec_sccs[0].energy.electrostatic.long_range.magnitude == approx( + -1.6079680663895344e30 + ) + assert sec_sccs[-1].energy.van_der_waals.value.magnitude == approx( + 2.5995702480888255e30 + ) + assert sec_sccs[-1].energy.van_der_waals.short_range.magnitude == approx( + 2.675488981642447e30 + ) + assert sec_sccs[-1].energy.van_der_waals.long_range.magnitude == approx( + -4.4191382265877185e28 + ) + assert sec_sccs[-1].energy.van_der_waals.correction.magnitude == approx( + -3.172735128774431e28 + ) + assert sec_sccs[0].energy.pressure_volume_work.value.magnitude == approx( + 5.46058641332406e26 + ) + + assert sec_sccs[0].forces.total.value[5][2].magnitude == approx( + -7.932968909721231e-10 + ) sec_systems = sec_run.system assert len(sec_systems) == 2 @@ -104,32 +143,56 @@ def test_md_verbose(parser): sec_method = sec_run.method assert len(sec_method) == 1 assert len(sec_method[0].force_field.model[0].contributions) == 8 - assert sec_method[0].force_field.model[0].contributions[6].type == 'bond' + assert sec_method[0].force_field.model[0].contributions[6].type == "bond" assert sec_method[0].force_field.model[0].contributions[6].n_interactions == 1017 assert sec_method[0].force_field.model[0].contributions[6].n_atoms == 2 - assert sec_method[0].force_field.model[0].contributions[6].atom_labels[10][0] == 'C' - assert sec_method[0].force_field.model[0].contributions[6].atom_indices[100][1] == 141 - assert sec_method[0].force_field.model[0].contributions[6].parameters[858] == approx(0.9999996193044006) + assert sec_method[0].force_field.model[0].contributions[6].atom_labels[10][0] == "C" + assert ( + sec_method[0].force_field.model[0].contributions[6].atom_indices[100][1] == 141 + ) + assert sec_method[0].force_field.model[0].contributions[6].parameters[ + 858 + ] == approx(0.9999996193044006) assert sec_method[0].force_field.force_calculations.vdw_cutoff.magnitude == 1.2e-09 - assert sec_method[0].force_field.force_calculations.vdw_cutoff.units == 'meter' - assert sec_method[0].force_field.force_calculations.coulomb_type == 'particle_mesh_ewald' + assert sec_method[0].force_field.force_calculations.vdw_cutoff.units == "meter" + assert ( + sec_method[0].force_field.force_calculations.coulomb_type + == "particle_mesh_ewald" + ) assert sec_method[0].force_field.force_calculations.coulomb_cutoff.magnitude == 0.9 - assert sec_method[0].force_field.force_calculations.coulomb_cutoff.units == 'meter' - assert sec_method[0].force_field.force_calculations.neighbor_searching.neighbor_update_frequency == 5 - assert sec_method[0].force_field.force_calculations.neighbor_searching.neighbor_update_cutoff.magnitude == 9.000000000000001e-10 - assert sec_method[0].force_field.force_calculations.neighbor_searching.neighbor_update_cutoff.units == 'meter' + assert sec_method[0].force_field.force_calculations.coulomb_cutoff.units == "meter" + assert ( + sec_method[ + 0 + ].force_field.force_calculations.neighbor_searching.neighbor_update_frequency + == 5 + ) + assert ( + sec_method[ + 0 + ].force_field.force_calculations.neighbor_searching.neighbor_update_cutoff.magnitude + == 9.000000000000001e-10 + ) + assert ( + sec_method[ + 0 + ].force_field.force_calculations.neighbor_searching.neighbor_update_cutoff.units + == "meter" + ) def test_md_edr(parser): archive = EntryArchive() - parser.parse('tests/data/gromacs/fe_test/mdrun.out', archive, None) + parser.parse("tests/data/gromacs/fe_test/mdrun.out", archive, None) assert len(archive.run[0].calculation) == 5 def test_md_atomsgroup(parser): archive = EntryArchive() - parser.parse('tests/data/gromacs/polymer_melt/step4.0_minimization.log', archive, None) + parser.parse( + "tests/data/gromacs/polymer_melt/step4.0_minimization.log", archive, None + ) sec_run = archive.run[0] sec_systems = sec_run.system @@ -137,55 +200,247 @@ def test_md_atomsgroup(parser): assert len(sec_systems[0].atoms_group) == 1 assert len(sec_systems[0].atoms_group[0].atoms_group) == 100 - assert sec_systems[0].atoms_group[0].label == 'group_S1P1' - assert sec_systems[0].atoms_group[0].type == 'molecule_group' + assert sec_systems[0].atoms_group[0].label == "group_S1P1" + assert sec_systems[0].atoms_group[0].type == "molecule_group" assert sec_systems[0].atoms_group[0].index == 0 - assert sec_systems[0].atoms_group[0].composition_formula == 'S1P1(100)' + assert sec_systems[0].atoms_group[0].composition_formula == "S1P1(100)" assert sec_systems[0].atoms_group[0].n_atoms == 7200 assert sec_systems[0].atoms_group[0].atom_indices[5] == 5 assert sec_systems[0].atoms_group[0].is_molecule is False - assert sec_systems[0].atoms_group[0].atoms_group[52].label == 'S1P1' - assert sec_systems[0].atoms_group[0].atoms_group[52].type == 'molecule' + assert sec_systems[0].atoms_group[0].atoms_group[52].label == "S1P1" + assert sec_systems[0].atoms_group[0].atoms_group[52].type == "molecule" assert sec_systems[0].atoms_group[0].atoms_group[52].index == 52 - assert sec_systems[0].atoms_group[0].atoms_group[52].composition_formula == 'ETHOX(10)' + assert ( + sec_systems[0].atoms_group[0].atoms_group[52].composition_formula == "ETHOX(10)" + ) assert sec_systems[0].atoms_group[0].atoms_group[52].n_atoms == 72 assert sec_systems[0].atoms_group[0].atoms_group[52].atom_indices[8] == 3752 assert sec_systems[0].atoms_group[0].atoms_group[52].is_molecule is True - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].label == 'group_ETHOX' - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].type == 'monomer_group' + assert ( + sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].label + == "group_ETHOX" + ) + assert ( + sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].type + == "monomer_group" + ) assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].index == 0 - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].composition_formula == 'ETHOX(10)' + assert ( + sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].composition_formula + == "ETHOX(10)" + ) assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].n_atoms == 72 - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atom_indices[5] == 5477 - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].is_molecule is False + assert ( + sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atom_indices[5] + == 5477 + ) + assert ( + sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].is_molecule + is False + ) - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].label == 'ETHOX' - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].type == 'monomer' - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].index == 7 - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].composition_formula == 'C(2)H(4)O(1)' - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].n_atoms == 7 - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].atom_indices[5] == 5527 - assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].is_molecule is False + assert ( + sec_systems[0] + .atoms_group[0] + .atoms_group[76] + .atoms_group[0] + .atoms_group[7] + .label + == "ETHOX" + ) + assert ( + sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].type + == "monomer" + ) + assert ( + sec_systems[0] + .atoms_group[0] + .atoms_group[76] + .atoms_group[0] + .atoms_group[7] + .index + == 7 + ) + assert ( + sec_systems[0] + .atoms_group[0] + .atoms_group[76] + .atoms_group[0] + .atoms_group[7] + .composition_formula + == "C(2)H(4)O(1)" + ) + assert ( + sec_systems[0] + .atoms_group[0] + .atoms_group[76] + .atoms_group[0] + .atoms_group[7] + .n_atoms + == 7 + ) + assert ( + sec_systems[0] + .atoms_group[0] + .atoms_group[76] + .atoms_group[0] + .atoms_group[7] + .atom_indices[5] + == 5527 + ) + assert ( + sec_systems[0] + .atoms_group[0] + .atoms_group[76] + .atoms_group[0] + .atoms_group[7] + .is_molecule + is False + ) def test_geometry_optimization(parser): archive = EntryArchive() - parser.parse('tests/data/gromacs/polymer_melt/step4.0_minimization.log', archive, None) + parser.parse( + "tests/data/gromacs/polymer_melt/step4.0_minimization.log", archive, None + ) sec_workflow = archive.workflow2 - assert sec_workflow.method.type == 'atomic' - assert sec_workflow.method.method == 'steepest_descent' - assert sec_workflow.method.convergence_tolerance_force_maximum.magnitude == approx(6.02214076e+38) - assert sec_workflow.method.convergence_tolerance_force_maximum.units == 'newton' - assert sec_workflow.results.final_force_maximum.magnitude == approx(1.303670442204273e+38) - assert sec_workflow.results.final_force_maximum.units == 'newton' + assert sec_workflow.method.type == "atomic" + assert sec_workflow.method.method == "steepest_descent" + assert sec_workflow.method.convergence_tolerance_force_maximum.magnitude == approx( + 6.02214076e38 + ) + assert sec_workflow.method.convergence_tolerance_force_maximum.units == "newton" + assert sec_workflow.results.final_force_maximum.magnitude == approx( + 1.303670442204273e38 + ) + assert sec_workflow.results.final_force_maximum.units == "newton" assert sec_workflow.results.optimization_steps == 12 assert sec_workflow.method.optimization_steps_maximum == 5000 assert len(sec_workflow.results.energies) == 11 - assert sec_workflow.results.energies[2].magnitude == approx(2.9900472759121395e+31) - assert sec_workflow.results.energies[2].units == 'joule' + assert sec_workflow.results.energies[2].magnitude == approx(2.9900472759121395e31) + assert sec_workflow.results.energies[2].units == "joule" assert len(sec_workflow.results.steps) == 11 assert sec_workflow.results.steps[4] == 5000 + + +def test_integrator_sd(parser): + archive = EntryArchive() + parser.parse( + "tests/data/gromacs/water_AA_ENUM_tests/integrator-sd/md.log", archive, None + ) + + sec_run = archive.run[0] + # assert sec_run.program.version == "2018.6" + + sec_workflow = archive.workflow2 + assert sec_workflow.m_def.name == "MolecularDynamics" + sec_method = sec_workflow.method + assert sec_method.thermodynamic_ensemble == "NVT" + assert sec_method.integrator_type == "langevin_goga" + assert sec_method.thermostat_parameters[0].thermostat_type == "langevin_goga" + assert sec_method.thermostat_parameters[0].reference_temperature.magnitude == 298.0 + assert sec_method.thermostat_parameters[0].coupling_constant.magnitude == 5e-13 + + +def test_integrator_mdvv(parser): + archive = EntryArchive() + parser.parse( + "tests/data/gromacs/water_AA_ENUM_tests/integrator-mdvv/md.log", archive, None + ) + + sec_run = archive.run[0] + # assert sec_run.program.version == "2018.6" + + sec_workflow = archive.workflow2 + assert sec_workflow.m_def.name == "MolecularDynamics" + sec_method = sec_workflow.method + assert sec_method.thermodynamic_ensemble == "NVE" + assert sec_method.integrator_type == "velocity_verlet" + + +def test_integrator_bd(parser): + archive = EntryArchive() + parser.parse( + "tests/data/gromacs/water_AA_ENUM_tests/integrator-bd/md.log", archive, None + ) + + sec_run = archive.run[0] + # assert sec_run.program.version == "2018.6" + + sec_workflow = archive.workflow2 + assert sec_workflow.m_def.name == "MolecularDynamics" + sec_method = sec_workflow.method + assert sec_method.thermodynamic_ensemble == "NVE" + assert sec_method.integrator_type == "brownian" + + +# TODO test for andersen thermostat? It's not clear how to run this at the moment or if it is deprecated in newer versions of Gromacs. + + +def test_integrator_md_thermostat_vrescale(parser): + archive = EntryArchive() + parser.parse( + "tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-vrescale/md.log", + archive, + None, + ) + + sec_run = archive.run[0] + assert sec_run.program.version == "2018.6" + + sec_workflow = archive.workflow2 + assert sec_workflow.m_def.name == "MolecularDynamics" + sec_method = sec_workflow.method + assert sec_method.thermodynamic_ensemble == "NVT" + assert sec_method.integrator_type == "leap_frog" + assert sec_method.thermostat_parameters[0].thermostat_type == "velocity_rescaling" + assert sec_method.thermostat_parameters[0].reference_temperature.magnitude == 298.0 + assert sec_method.thermostat_parameters[0].coupling_constant.magnitude == 5e-13 + + +def test_integrator_md_thermostat_nosehoover_barostat_parrinellorahman(parser): + archive = EntryArchive() + parser.parse( + "tests/data/gromacs/water_AA_ENUM_tests/integrator-md/thermostat-nosehoover_barostat-parrinellorahman/md.log", + archive, + None, + ) + + sec_run = archive.run[0] + assert sec_run.program.version == "2018.6" + + sec_workflow = archive.workflow2 + assert sec_workflow.m_def.name == "MolecularDynamics" + sec_method = sec_workflow.method + assert sec_method.thermodynamic_ensemble == "NPT" + assert sec_method.integrator_type == "leap_frog" + assert sec_method.thermostat_parameters[0].thermostat_type == "nose_hoover" + assert sec_method.thermostat_parameters[0].reference_temperature.magnitude == 298.0 + assert sec_method.thermostat_parameters[0].coupling_constant.magnitude == 5e-13 + assert sec_method.barostat_parameters[0].barostat_type == "parrinello_rahman" + assert sec_method.barostat_parameters[0].coupling_type == "isotropic" + assert np.all( + sec_method.barostat_parameters[0].reference_pressure.magnitude + == [[100000.0, 0.0, 0.0], [0.0, 100000.0, 0.0], [0.0, 0.0, 100000.0]] + ) + assert np.all( + sec_method.barostat_parameters[0].coupling_constant.magnitude + == [ + [5.0e-12, 5.0e-12, 5.0e-12], + [5.0e-12, 5.0e-12, 5.0e-12], + [5.0e-12, 5.0e-12, 5.0e-12], + ] + ) + assert np.all( + sec_method.barostat_parameters[0].compressibility.magnitude + == [ + [7.4e-10, 0.0e00, 0.0e00], + [0.0e00, 7.4e-10, 0.0e00], + [0.0e00, 0.0e00, 7.4e-10], + ] + )