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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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Journal ArticleDOI
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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Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities
TL;DR: In molecular dynamics (MD) when constant- energy (NVE) simulations of Newton's equations of motion are attempted using the multiple time stepping Verlet-I/r-RESPA/Impulse, there are nonlinear instabilities when the longest step size is a third or possibly a fourth of the period of the fastest motion in the system.
Journal ArticleDOI
Molecular Dynamics Study of Bacteriorhodopsin and the Purple Membrane
TL;DR: It is shown that free energy perturbation theory can place water molecules in bR, with results that compare well with the observed water molecules, and a preliminary simulation illustrates that water molecules may indeed be displaced during the photocycle, after retinal undergoes an all-trans f 13-cis isomerization, and that this displacement may constitute a mechanism for proton pumping.
Journal ArticleDOI
Taxonomy of dynamic task scheduling schemes in distributed computing systems
TL;DR: The author presents a taxonomy of dynamic task scheduling schemes that is synthesised by treating state estimation and decision making as orthogonal problems that is regular, easily understood, compact, and its wide applicability is demonstrated by means of examples that encompass solutions proposed in the literature.
Journal ArticleDOI
Simulation-based performance prediction for large parallel machines
TL;DR: A performance prediction environment for large scale computers such as the Blue Gene machine that consists of a parallel simulator, BigSim, for predicting performance of machines with a very large number of processors, and BigNetSim, which incorporates a pluggable module of a detailed contention-based network model.
Research Letter Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer
TL;DR: Structural features of the aquaporin‐1 water channel important for its biological function, including the Asn‐Pro‐Ala (NPA) motifs, and the diffusion of water molecules into the channels were investigated, revealing the formation of single file water inside the channels for certain relative positions of the NPA motifs.
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