Journal ArticleDOI
General purpose molecular dynamics simulations fully implemented on graphics processing units
TLDR
This paper develops a general purpose molecular dynamics code that runs entirely on a single GPU and shows that the GPU implementation provides a performance equivalent to that of fast 30 processor core distributed memory cluster.About:
This article is published in Journal of Computational Physics.The article was published on 2008-05-01. It has received 1514 citations till now. The article focuses on the topics: GPU cluster & CUDA Pinned memory.read more
Citations
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Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Journal ArticleDOI
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
Robert T. McGibbon,Kyle A. Beauchamp,Matthew P. Harrigan,Christoph Klein,Jason M. Swails,Carlos X. Hernández,Christian R. Schwantes,Lee-Ping Wang,Thomas J. Lane,Vijay S. Pande +9 more
TL;DR: MDTraj is a modern, lightweight, and fast software package for analyzing MD simulations that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
Journal ArticleDOI
Cohesin Loss Eliminates All Loop Domains
Suhas S.P. Rao,Suhas S.P. Rao,Su Chen Huang,Brian Glenn St Hilaire,Brian Glenn St Hilaire,Jesse M. Engreitz,Elizabeth M. Perez,Kyong-Rim Kieffer-Kwon,Adrian L. Sanborn,Adrian L. Sanborn,Adrian L. Sanborn,Sarah E. Johnstone,Sarah E. Johnstone,Gavin D. Bascom,Ivan D. Bochkov,Xingfan Huang,Xingfan Huang,Muhammad S. Shamim,Muhammad S. Shamim,Jaeweon Shin,Jaeweon Shin,Douglass Turner,Douglass Turner,Ziyi Ye,Ziyi Ye,Arina D. Omer,James T. Robinson,James T. Robinson,James T. Robinson,Tamar Schlick,Tamar Schlick,Tamar Schlick,Bradley E. Bernstein,Bradley E. Bernstein,Rafael Casellas,Eric S. Lander,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +38 more
TL;DR: In this paper, the effects of degrading cohesin were explored, showing that loop domains can be eliminated and re-formed in under an hour, consistent with a model where loop extrusion is rapid.
Journal ArticleDOI
Biomolecular Simulation: A Computational Microscope for Molecular Biology
TL;DR: The rapidly evolving state of the art for atomic-level biomolecular simulation is described, the types of biological discoveries that can now be made through simulation are illustrated, and challenges motivating continued innovation in this field are discussed.
Book ChapterDOI
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
TL;DR: GROMACS as mentioned in this paper is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world.
References
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Journal ArticleDOI
Fast parallel algorithms for short-range molecular dynamics
TL;DR: In this article, three parallel algorithms for classical molecular dynamics are presented, which can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Journal ArticleDOI
Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.