Note
Molecular Dynamics productivity environment includes a set of tools which are needed for scientific computing and visualization in the respective domain. The following is an attempt to define which ones are relevant for the HPCBIOS communities and set an action plan.
- BC Policy: HPCBIOS_2012-95
- Date of Policy: 2012-12-15
The main objective of this policy is to provide the following common productivity environment across any HPCBIOS resources:
| Name | Prefered version(s) | Compliance level | Reference |
|---|---|---|---|
| GROMACS | v4.5.5 or later | MUST | http://www.gromacs.org |
| CP2K | 20111205 or latest | MUST | http://www.cp2k.org |
| CHARMM | c37b2 | SHOULD | http://www.charmm.org |
| NAMD | v2.8 | MUST | http://www.ks.uiuc.edu/Research/namd |
| VMD | v1.9 | SHOULD | http://www.ks.uiuc.edu/Research/vmd |
| DL_POLY | v4.02 | SHOULD | http://www.ccp5.ac.uk/DL_POLY |
| LAMMPS | v1Feb2014 or later | SHOULD | http://lammps.sandia.gov |
| CPMD | v3.15.1 | SHOULD | http://www.cpmd.org |
| NWCHEM | v6.1 | SHOULD | http://www.nwchem-sw.org |
| XMakemol | v5.16 | SHOULD | http://www.nongnu.org/xmakemol |
| TINKER | v6.0.08 | SHOULD | http://dasher.wustl.edu/tinker/ |
| HOOMD-blue | v0.10.0 | SHOULD | http://codeblue.umich.edu/hoomd-blue/ |
| AMBER | v11 | SHOULD | http://ambermd.org |
This productivity environment will be supplemented with other related productivity tools as they become available on allocated systems.
Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS maintainers.