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Scalable Molecular Dynamics with NAMD
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The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark Abraham,Teemu Murtola,Roland Schulz,Roland Schulz,Szilárd Páll,Jeremy C. Smith,Jeremy C. Smith,Berk Hess,Erik Lindahl,Erik Lindahl +9 more
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
Gromacs 4.5
Sander Pronk,Szilárd Páll,Szilárd Páll,Roland Schulz,Roland Schulz,Per Larsson,Pär Bjelkmar,Pär Bjelkmar,Rossen Apostolov,Rossen Apostolov,Michael R. Shirts,Jeremy C. Smith,Jeremy C. Smith,Peter M. Kasson,David van der Spoel,David van der Spoel,Berk Hess,Berk Hess,Erik Lindahl,Erik Lindahl,Erik Lindahl +20 more
TL;DR: A range of new simulation algorithms and features developed during the past 4 years are presented, leading up to the GROMACS 4.5 software package, which provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
Journal ArticleDOI
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
Kenno Vanommeslaeghe,Elizabeth Hatcher,Chayan Acharya,Sibsankar Kundu,Shijun Zhong,Jihyun Shim,Eva Darian,Olgun Guvench,Pedro E. M. Lopes,Igor Vorobyov,Alexander D. MacKerell +10 more
TL;DR: An extension of the CHARMM force field to drug‐like molecules is presented, making it possible to perform “all‐CHARMM” simulations on drug‐target interactions thereby extending the utility ofCHARMM force fields to medicinally relevant systems.
Journal ArticleDOI
CHARMM-GUI: a web-based graphical user interface for CHARMM.
TL;DR: The CHARMM-GUI as mentioned in this paper is a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM.
References
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AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
Paul K. Weiner,Peter A. Kollman +1 more
TL;DR: A computer program to build models of molecules and calculate their interactions using empirical energy approaches is described, sufficiently flexible and general to allow modeling of small molecules, as well as polymers.
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The Tau Parallel Performance System
Sameer Shende,Allen D. Malony +1 more
TL;DR: This paper presents the TAU (Tuning and Analysis Utilities) parallel performance sytem and describes how it addresses diverse requirements for performance observation and analysis.
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Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality.
Jan Liphardt,Sophie Dumont,Steven B. Smith,Ignacio Tinoco,Carlos Bustamante,Carlos Bustamante +5 more
TL;DR: The implementation and test of Jarzynski's equality provides the first example of its use as a bridge between the statistical mechanics of equilibrium and nonequilibrium systems, and extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments.
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Mitigation strategies for pandemic influenza in the United States
TL;DR: A large-scale stochastic simulation model is introduced and used to investigate the spread of a pandemic strain of influenza virus through the U.S. population and suggests that the rapid production and distribution of vaccines could significantly slow disease spread and limit the number ill to <10% of the population, particularly if children are preferentially vaccinated.
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TREESPH: A Unification of SPH with the Hierarchical Tree Method
Lars Hernquist,Neal Katz +1 more
TL;DR: In this paper, a general-purpose code for evolving three-dimensional, self-gravitating fluids in astrophyics, both with and without collisionless matter, is described.
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