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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
Citations
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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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Force-clamp spectroscopy monitors the folding trajectory of a single protein.
Julio M. Fernandez,Hongbin Li +1 more
TL;DR: Direct observations of the complete folding trajectory of a protein provide a benchmark to determine the physical basis of the folding reaction at the single-molecule level.
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Creating synthetic baseline populations
TL;DR: In this paper, the authors presented a method to estimate the proportion of households in a block group or census tract with a desired combination of demographics by selecting households from the associated PUMS according to these proportions.
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NAMD: a Parallel, Object-Oriented Molecular Dynamics Program
Mark T. Nelson,William Humphrey,Attila Gursoy,Andrew Dalke,Laxmikant V. Kale,Robert D. Skeel,Klaus Schulten +6 more
TL;DR: NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers that uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors.
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The Case of the Missing Supercomputer Performance: Achieving Optimal Performance on the 8,192 Processors of ASCI Q
TL;DR: This paper describes how to improved the effective performance of ASCI Q, the world's second-fastest supercomputer, to meet expectations and provides insight into performance analysis that is immediately applicable to other large-scale supercomputers.
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