Open AccessBook
Scalable Molecular Dynamics with NAMD
About:
The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
Citations
More filters
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
More filters
Journal ArticleDOI
Application of the Ewald method to cosmological N-body simulations
TL;DR: In this paper, conditions aux limites periodiques sont introduced in un code de N corps cosmologique avec la methode Elwald, and l'evolution lineaire des fluctuations de densite est en accord avec les calculs analytiques.
Journal ArticleDOI
Mechanisms of Selectivity in Channels and Enzymes Studied with Interactive Molecular Dynamics
TL;DR: Interactive molecular dynamics, a new modeling tool for rapid investigation of the physical mechanisms of biological processes at the atomic level, is applied to study selectivity and regulation of the membrane channel protein GlpF and the enzyme glycerol kinase.
Achieving High Performance on Extremely Large Parallel Machines: Performance Prediction and Load Balancing
TL;DR: This thesis explores Parallel Discrete Event Simulation (PDES) techniques with an optimistic synchronization protocol to simulate parallel applications running on a very large number of processors and optimize the synchronization protocol by exploiting the inherent determinacy that is normally found in parallel applications to reduce the synchronization overhead significantly.
Journal ArticleDOI
The reduced cell multipole method for Coulomb interactions in periodic systems with million-atom unit cells
TL;DR: The reduced cell multipole method as discussed by the authors is 38 times faster than the Ewald method for a 4816-atom (unit cell) system and scales linearly with the number of atoms in the cell.
Related Papers (5)
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell,D. Bashford,M. Bellott,Roland L. Dunbrack,Jeffrey D. Evanseck,Martin J. Field,Stefan Fischer,Jiali Gao,H. Guo,S. Ha,Diane Joseph-McCarthy,L. Kuchnir,K. Kuczera,F. T. K. Lau,C. Mattos,Stephen W. Michnick,Thien H. Ngo,D. T. Nguyen,B. Prodhom,W. E. Reiher,Benoît Roux,M. Schlenkrich,Jeremy C. Smith,Roland H. Stote,John E. Straub,Masakatsu Watanabe,J. Wiórkiewicz-Kuczera,D. Yin,Martin Karplus +28 more