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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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Object-Based Adaptive Load Balancing for MPI Programs∗
TL;DR: An implementation of MPI, called Adaptive MPI (AMPI), that supports dynamic load balancing and multithreading for MPI applications and is based on the user-level migrating threads and load balancing capabilities provided by the Charm++ framework.
Book ChapterDOI
An Efficient and Transparent Thread Migration Scheme in the PM2 Runtime System
TL;DR: A new iso-address approach to the dynamic allocation of data in a multithreaded runtime system with thread migration capability that guarantees that the migrated threads and their associated static data are relocated exactly at the same virtual address on the destination nodes.
Proceedings ArticleDOI
Pentium Pro Inside: I. A Treecode at 430 Gigaflops on ASCI Red, II. Price/Performance of $50/Mflop on Loki and Hyglac
TL;DR: Two methods of solving the gravitational N-body problem on ASCI Red and two simulations which sustained roughly one Gigaflop on each of two 16 processor Beowulf-class computers constructed entirely from commodity personal computer technology for $50k each in September, 1996 are presented.
Journal ArticleDOI
Dynamic load-balancing of finite element applications with the DRAMA library
Achim Basermann,Jean Clinckemaillie,Thierry Coupez,Jochen Fingberg,Hugues Digonnet,Richard Ducloux,Jean-Marc Gratien,Ulrich Hartmann,G. Lonsdale,Bart Maerten,Dirk Roose,Chris Walshaw +11 more
TL;DR: The main body of the paper will demonstrate the ability to provide dynamic load-balancing for parallel FEM problems that include: adaptive meshing, re-meshing, the need for multi-phase partitioning.
Journal ArticleDOI
Ab initio design of high-k dielectrics: La(x)Y1-xAlO3.
TL;DR: It is shown that aluminates LaxY1-xAlO3 alloys derived by mixing aluminum oxide with lanthanum and yttrium oxides have unique physical attributes for a possible application as gate dielectrics when stabilized in the rhombohedral perovskite structure, and which are lost in the orthorhombic modification.
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