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abin.bib
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@article{Martyna1996,
author = {Martyna, Glenn J and Tuckerman, Mark E and Tobias, Douglas J and Klein, Michael L},
doi = {10.1080/00268979600100761},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/Molecular Physics/Martyna et al/Martyna et al. - 1996 - Explicit reversible integrators for extended systems dynamics.pdf:pdf},
isbn = {0026-8976},
issn = {0026-8976},
journal = {Mol. Phys.},
keywords = {,algorithms,behavior,canonical ensemble,crystal-structure,hybrid monte-carlo,molecular-dynamics,path-integrals,simulations,temperature},
language = {English},
month = {apr},
number = {5},
pages = {1117--1157},
title = {{Explicit reversible integrators for extended systems dynamics}},
url = {{\textless}Go to ISI{\textgreater}://A1996UE44300011 http://www.tandfonline.com/doi/abs/10.1080/00268979600100761 {\{}{\textless}{\}}Go to ISI{\{}{\textgreater}{\}}://A1996UE44300011},
volume = {87},
year = {1996}
}
@phdthesis{Ceriotti2010d,
author = {Ceriotti, Michele},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/Unknown/Ceriotti/Ceriotti - 2010 - A novel framework for enhanced molecular dynamics based on the generalized Langevin equation Molecular dynamics simula.pdf:pdf},
keywords = {GLE},
mendeley-tags = {GLE},
pages = {145},
school = {ETH Z{\"{u}}rich},
title = {{A novel framework for enhanced molecular dynamics based on the generalized Langevin equation Molecular dynamics simulations Simulation of the trajectories of a system at the atomic level}},
year = {2010}
}
@article{Ceriotti2012,
author = {Ceriotti, Michele and Manolopoulos, David E.},
doi = {10.1103/PhysRevLett.109.100604},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/Physical Review Letters/Ceriotti, Manolopoulos/Ceriotti, Manolopoulos - 2012 - Efficient First-Principles Calculation of the Quantum Kinetic Energy and Momentum Distribution of Nuclei.pdf:pdf;:home/hollas/Documents/Mendeley{\_}Desktop/Physical Review Letters/Ceriotti, Manolopoulos/Ceriotti, Manolopoulos - 2012 - Efficient First-Principles Calculation of the Quantum Kinetic Energy and Momentum Distribution of Nuclei.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {sep},
number = {10},
pages = {100604},
title = {{Efficient First-Principles Calculation of the Quantum Kinetic Energy and Momentum Distribution of Nuclei}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.109.100604},
volume = {109},
year = {2012}
}
@article{Bonhommeau2014,
author = {Bonhommeau, David A. and Lewerenz, Marius and Gaigeot, Marie-Pierre},
doi = {10.1016/j.cpc.2013.09.026},
issn = {00104655},
journal = {Comput. Phys. Commun.},
month = {mar},
number = {3},
pages = {1188--1191},
title = {{MCMC2 (version 1.1): A Monte Carlo code for multiply-charged clusters}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0010465513003305},
volume = {185},
year = {2014}
}
@article{Shao2006,
abstract = {Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.},
author = {Shao, Yihan and Molnar, Laszlo Fusti and Jung, Yousung and Kussmann, J{\"{o}}rg and Ochsenfeld, Christian and Brown, Shawn T. and Gilbert, Andrew T.B. B and Slipchenko, Lyudmila V. and Levchenko, Sergey V. and O'Neill, Darragh P. and {DiStasio Jr}, Robert A. and Lochan, Rohini C. and Wang, Tao and Beran, Gregory J.O. O and Besley, Nicholas A. and Herbert, John M. and {Yeh Lin}, Ching and {Van Voorhis}, Troy and {Hung Chien}, Siu and Sodt, Alex and Steele, Ryan P. and Rassolov, Vitaly A. and Maslen, Paul E. and Korambath, Prakashan P. and Adamson, Ross D. and Austin, Brian and Baker, Jon and Byrd, Edward F. C. and Dachsel, Holger and Doerksen, Robert J. and Dreuw, Andreas and Dunietz, Barry D. and Dutoi, Anthony D. and Furlani, Thomas R. and Gwaltney, Steven R. and Heyden, Andreas and Hirata, So and Hsu, Chao-Ping and Kedziora, Gary and Khalliulin, Rustam Z. and Klunzinger, Phil and Lee, Aaron M. and Lee, Michael S. and Liang, Wanzhen and Lotan, Itay and Nair, Nikhil and Peters, Baron and Proynov, Emil I. and Pieniazek, Piotr A. and {Min Rhee}, Young and Ritchie, Jim and Rosta, Edina and {David Sherrill}, C. and Simmonett, Andrew C. and Subotnik, Joseph E. and {Lee Woodcock III}, H. and Zhang, Weimin and Bell, Alexis T. and Chakraborty, Arup K. and Chipman, Daniel M. and Keil, Frerich J. and Warshel, Arieh and Hehre, Warren J. and {Schaefer III}, Henry F. and Kong, Jing and Krylov, Anna I. and Gill, Peter M. W. and Head-Gordon, Martin and O'Neill, Darragh P and DiStasio, Robert A and Lochan, Rohini C. and Wang, Tao and Beran, Gregory J.O. O and Besley, Nicholas A. and Herbert, John M. and Lin, Ching Yeh and {Van Voorhis}, Troy and Chien, Siu Hung and Sodt, Alex and Steele, Ryan P. and Rassolov, Vitaly A. and Maslen, Paul E. and Korambath, Prakashan P. and Adamson, Ross D. and Austin, Brian and Baker, Jon and Byrd, Edward F. C. and Dachsel, Holger and Doerksen, Robert J. and Dreuw, Andreas and Dunietz, Barry D. and Dutoi, Anthony D. and Furlani, Thomas R. and Gwaltney, Steven R. and Heyden, Andreas and Hirata, So and Hsu, Chao-Ping and Kedziora, Gary and Khalliulin, Rustam Z. and Klunzinger, Phil and Lee, Aaron M. and Lee, Michael S. and Liang, Wanzhen and Lotan, Itay and Nair, Nikhil and Peters, Baron and Proynov, Emil I. and Pieniazek, Piotr A. and Rhee, Young Min and Ritchie, Jim and Rosta, Edina and Sherrill, C David and Simmonett, Andrew C. and Subotnik, Joseph E. and Woodcock, H Lee and Zhang, Weimin and Bell, Alexis T. and Chakraborty, Arup K. and Chipman, Daniel M. and Keil, Frerich J. and Warshel, Arieh and Hehre, Warren J. and Schaefer, Henry F and Kong, Jing and Krylov, Anna I. and Gill, Peter M. W. and Head-Gordon, Martin},
doi = {10.1039/b517914a},
issn = {1463-9076},
journal = {Phys. Chem. Chem. Phys.},
keywords = {Algorithms,Biophysics,Biophysics: methods,Chemical,Cluster Analysis,Electrons,Magnetic Resonance Spectroscopy,Models,Quantum Theory,Thermodynamics},
month = {jul},
number = {27},
pages = {3172--3191},
pmid = {16902710},
title = {{Advances in methods and algorithms in a modern quantum chemistry program package.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16902710 http://xlink.rsc.org/?DOI=B517914A},
volume = {8},
year = {2006}
}
@article{Ufimtsev2008,
abstract = {The paper provide a brief overview of electronic structure theory and details the implementation of quantum chemistry methods on a graphical processing unit. The paper also analyze algorithm performance in terms of floating-point operations and memory bandwidth, and assess the adequacy of single-precision accuracy for quantum chemistry applications.},
author = {Ufimtsev, Ivan S. and Mart{\'{i}}nez, Todd J.},
doi = {10.1109/MCSE.2008.148},
isbn = {1521-9615},
issn = {1521-9615},
journal = {Comput. Sci. Eng.},
month = {nov},
number = {6},
pages = {26--34},
title = {{Graphical Processing Units for Quantum Chemistry}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4653202},
volume = {10},
year = {2008}
}
@article{Ceriotti2010,
author = {Ceriotti, Michele and Bussi, Giovanni and Parrinello, Michele},
doi = {10.1021/ct900563s},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/J. Chem. Theory Comput/Ceriotti, Bussi, Parrinello/Ceriotti, Bussi, Parrinello - 2010 - Colored-Noise Thermostats a la Carte.pdf:pdf},
issn = {1549-9618},
journal = {J. Chem. Theory Comput.},
month = {apr},
number = {4},
pages = {1170--1180},
title = {{Colored-Noise Thermostats a la Carte}},
url = {http://pubs.acs.org/doi/abs/10.1021/ct900563s},
volume = {6},
year = {2010}
}
@article{Barbatti2011,
author = {Barbatti, Mario},
doi = {10.1002/wcms.64},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/Wiley Interdisciplinary Reviews Computational Molecular Science/Barbatti/Barbatti - 2011 - Nonadiabatic dynamics with trajectory surface hopping method.pdf:pdf},
issn = {17590876},
journal = {Wiley Interdiscip. Rev. Comput. Mol. Sci.},
month = {jul},
number = {4},
pages = {620--633},
title = {{Nonadiabatic dynamics with trajectory surface hopping method}},
url = {http://doi.wiley.com/10.1002/wcms.64},
volume = {1},
year = {2011}
}
@article{Schmidt1993,
author = {Schmidt, Michael W. and Baldridge, Kim K. and Boatz, Jerry A. and Elbert, Steven T. and Gordon, Mark S. and Jensen, Jan H. and Koseki, Shiro and Matsunaga, Nikita and Nguyen, Kiet A. and Su, Shujun and Windus, Theresa L. and Dupuis, Michel and Montgomery, John A.},
doi = {10.1002/jcc.540141112},
issn = {0192-8651},
journal = {J. Comput. Chem.},
keywords = {,GAMESS},
mendeley-tags = {GAMESS},
month = {nov},
number = {11},
pages = {1347--1363},
title = {{General atomic and molecular electronic structure system}},
url = {http://doi.wiley.com/10.1002/jcc.540141112},
volume = {14},
year = {1993}
}
@article{Martyna1992a,
author = {Martyna, Glenn J. and Klein, Michael L. and Tuckerman, Mark},
doi = {10.1063/1.463940},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/The Journal of Chemical Physics/Martyna, Klein, Tuckerman/Martyna, Klein, Tuckerman - 1992 - Nosé–Hoover chains The canonical ensemble via continuous dynamics.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {4},
pages = {2635--2643},
title = {{Nosé–Hoover chains: The canonical ensemble via continuous dynamics}},
url = {http://link.aip.org/link/JCPSA6/v97/i4/p2635/s1{\{}{\&}{\}}Agg=doi http://link.aip.org/link/JCPSA6/v97/i4/p2635/s1{\&}Agg=doi},
volume = {97},
year = {1992}
}
@misc{turbomole,
title = {{TURBOMOLE V6.4 2012, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com}}
}
@article{Hutter2014,
author = {Hutter, J{\"{u}}rg and Iannuzzi, Marcella and Schiffmann, Florian and VandeVondele, Joost},
doi = {10.1002/wcms.1159},
issn = {17590876},
journal = {Wiley Interdiscip. Rev. Comput. Mol. Sci.},
month = {jan},
number = {1},
pages = {15--25},
title = {cp2k: atomistic simulations of condensed matter systems},
url = {http://doi.wiley.com/10.1002/wcms.1159},
volume = {4},
year = {2014}
}
@article{Gotz2014,
abstract = {We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.},
author = {G{\"{o}}tz, Andreas W and Clark, Matthew a and Walker, Ross C},
doi = {10.1002/jcc.23444},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/Journal of computational chemistry/G{\"{o}}tz, Clark, Walker/G{\"{o}}tz, Clark, Walker - 2014 - An extensible interface for QMMM molecular dynamics simulations with AMBER.pdf:pdf},
issn = {1096-987X},
journal = {J. Comput. Chem.},
month = {jan},
number = {2},
pages = {95--108},
pmid = {24122798},
title = {{An extensible interface for QM/MM molecular dynamics simulations with AMBER.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24122798},
volume = {35},
year = {2014}
}
@article{Pittner2009,
author = {Pittner, Jiri and Lischka, Hans and Barbatti, Mario},
doi = {10.1016/j.chemphys.2008.10.013},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/Chemical Physics/Pittner, Lischka, Barbatti/Pittner, Lischka, Barbatti - 2009 - Optimization of mixed quantum-classical dynamics Time-derivative coupling terms and selected couplin.pdf:pdf},
issn = {03010104},
journal = {Chem. Phys.},
keywords = {,mixed-quantum classical dynamics,non-adiabatic coupling},
month = {feb},
number = {1-3},
pages = {147--152},
publisher = {Elsevier B.V.},
title = {{Optimization of mixed quantum-classical dynamics: Time-derivative coupling terms and selected couplings}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0301010408004783},
volume = {356},
year = {2009}
}
@misc{MOLPRO06,
address = {Cardiff, UK},
annote = {see http://www.molpro.net},
author = {Werner, H.-J. and Knowles, P J and Manby, F R and Sch{\"{u}}tz, M and Celani, P and Knizia, G and Korona, T and Lindh, R and Mitrushenkov, A and Rauhut, G and Adler, T B and Amos, R D and Bernhardsson, A and Berning, A and Cooper, D L and Deegan, M J O and Dobbyn, A J and Eckert, F and Goll, E and Hampel, C and Hesselmann, A and Hetzer, G and Hrenar, T and Jansen, G and K{\"{o}}ppl, C and Liu, Y and Lloyd, A W and Mata, R A and May, A J and McNicholas, S J and Meyer, W and Mura, M E and Nicklass, A and Palmieri, P and Pfl{\"{u}}ger, K and Pitzer, R and Reiher, M and Shiozaki, T and Stoll, H and Stone, A J and Tarroni, R and Thorsteinsson, T and Wang, M and Wolf, A and Others},
title = {{MOLPRO, version 2006.1, a package of ab initio programs}},
year = {2006}
}
@article{Neese2012,
author = {Neese, Frank},
doi = {10.1002/wcms.81},
issn = {17590876},
journal = {Wiley Interdiscip. Rev. Comput. Mol. Sci.},
month = {jan},
number = {1},
pages = {73--78},
title = {{The ORCA program system}},
url = {http://doi.wiley.com/10.1002/wcms.81},
volume = {2},
year = {2012}
}
@article{Ceriotti2011,
abstract = {The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zero-point energy effects can be included comparatively cheaply in simulations of harmonic and quasiharmonic systems by augmenting classical molecular dynamics with a generalized Langevin equation (GLE). Here we describe how a similar approach can be used to accelerate the convergence of path integral (PI) molecular dynamics to the exact quantum mechanical result in more strongly anharmonic systems exhibiting both zero point energy and tunnelling effects. The resulting PI-GLE method is illustrated with applications to a double-well tunnelling problem and to liquid water. (C) 2011 American Institute of Physics. [doi:10.1063/1.3556661]},
author = {Ceriotti, Michele and Manolopoulos, David E and Parrinello, Michele},
doi = {10.1063/1.3556661},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/J. Chem. Phys/Ceriotti, Manolopoulos, Parrinello/Ceriotti, Manolopoulos, Parrinello - 2011 - Accelerating the convergence of path integral dynamics with a generalized Langevin equati(2).pdf:pdf;:home/hollas/Documents/Mendeley{\_}Desktop/J. Chem. Phys/Ceriotti, Manolopoulos, Parrinello/Ceriotti, Manolopoulos, Parrinello - 2011 - Accelerating the convergence of path integral dynamics with a generalized Langevin equation.pdf:pdf},
issn = {1089-7690},
journal = {J. Chem. Phys.},
keywords = {Molecular Dynamics Simulation,Quantum Theory,Water,Water: chemistry},
month = {feb},
number = {8},
pages = {84104},
pmid = {21361524},
title = {{Accelerating the convergence of path integral dynamics with a generalized Langevin equation}},
url = {http://scitation.aip.org/content/aip/journal/jcp/134/8/10.1063/1.3556661 http://www.ncbi.nlm.nih.gov/pubmed/21361524},
volume = {134},
year = {2011}
}
@book{Tuckerman_book,
address = {Great Clarendon Street, Oxford},
author = {Tuckerman, M E},
publisher = {Oxford University Press},
title = {{Statistical Mechanics: Theory and Molecular Simulations}},
year = {2010}
}
@misc{G09,
annote = {Gaussian Inc. Wallingford CT},
author = {Frisch, M J and Trucks, G W and Schlegel, H B and Scuseria, G E and Robb, M A and Cheeseman, J R and Scalmani, G and Barone, V and Mennucci, B and Petersson, G A and Nakatsuji, H and Caricato, M and Li, X and Hratchian, H P and Izmaylov, A F and Bloino, J and Zheng, G and Sonnenberg, J L and Hada, M and Ehara, M and Toyota, K and Fukuda, R and Hasegawa, J and Ishida, M and Nakajima, T and Honda, Y and Kitao, O and Nakai, H and Vreven, T and {Montgomery Jr.}, J A and Peralta, J E and Ogliaro, F and Bearpark, M and Heyd, J J and Brothers, E and Kudin, K N and Staroverov, V N and Kobayashi, R and Normand, J and Raghavachari, K and Rendell, A and Burant, J C and Iyengar, S S and Tomasi, J and Cossi, M and Rega, N and Millam, J M and Klene, M and Knox, J E and Cross, J B and Bakken, V and Adamo, C and Jaramillo, J and Gomperts, R and Stratmann, R E and Yazyev, O and Austin, A J and Cammi, R and Pomelli, C and Ochterski, J W and Martin, R L and Morokuma, K and Zakrzewski, V G and Voth, G A and Salvador, P and Dannenberg, J J and Dapprich, S and Daniels, A D and Farkas, {\"{O}} and Foresman, J B and Ortiz, J V and Cioslowski, J and Fox, D J},
title = {{Gaussian 09 Revision A.1}},
year = {2009}
}
@article{Granucci2007,
author = {Granucci, Giovanni and Persico, Maurizio},
doi = {10.1063/1.2715585},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {13},
pages = {134114},
title = {{Critical appraisal of the fewest switches algorithm for surface hopping}},
url = {http://scitation.aip.org/content/aip/journal/jcp/126/13/10.1063/1.2715585},
volume = {126},
year = {2007}
}
@article{Yoshida1990,
abstract = {For Hamiltonian systems of the form H = T(p)+V(q) a method is shown to construct explicit and time reversible symplectic integrators of higher order. For any even order there exists at least one symplectic integrator with exact coefficients. The simplest one is the 4th order integrator which agrees with one found by Forest and by Neri. For 6th and 8th orders, symplectic integrators with fewer steps are obtained, for which the coefficients are given by solving a set of simultaneous algebraic equations numerically.},
author = {Yoshida, Haruo},
doi = {http://dx.doi.org/10.1016/0375-9601(90)90092-3},
issn = {0375-9601},
journal = {Phys. Lett. A},
month = {nov},
number = {5–7},
pages = {262--268},
title = {{Construction of higher order symplectic integrators}},
url = {http://www.sciencedirect.com/science/article/pii/0375960190900923},
volume = {150},
year = {1990}
}
@article{Ceriotti,
author = {Ceriotti, Michele and Bussi, Giovanni and Parrinello, Michele},
doi = {10.1103/PhysRevLett.103.030603},
file = {:home/hollas/Documents/Mendeley{\_}Desktop/Physical Review Letters/Ceriotti, Bussi, Parrinello/Ceriotti, Bussi, Parrinello - 2009 - Nuclear Quantum Effects in Solids Using a Colored-Noise Thermostat.pdf:pdf;:home/hollas/Documents/Mendeley{\_}Desktop/Unknown/Ceriotti, Bussi, Parrinello/Ceriotti, Bussi, Parrinello - Unknown - A tunable, all-purpose, colored-noise thermostat.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jul},
number = {3},
pages = {030603},
title = {{Nuclear Quantum Effects in Solids Using a Colored-Noise Thermostat}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.103.030603},
volume = {103},
year = {2009}
}