A hybrid algorithm for parallel molecular dynamics simulations
نویسندگان
چکیده
منابع مشابه
A hybrid algorithm for parallel molecular dynamics simulations
This article describes an algorithm for hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-ranged forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors ...
متن کاملHybrid Parallel Reactive Molecular Dynamics Simulations of HEHN Decomposition
This is simply an outline; the abstract will go here Keywords-thermal decomposition; HEHN; reactive molecular dynamics; hybrid parallelism;
متن کاملParallel Molecular Dynamics Simulations ofBiomolecular
We describe a general purpose parallel molecular dynamics code, for simulations of arbitrary mixtures of exible molecules in solution. The program allows us to simulate molecular systems described by standard force elds like AMBER, GROMOS or CHARMM, containing terms for short-range interactions of the Lennard-Jones type, electrostatic interactions, covalent bonds, covalent angles and torsional ...
متن کاملParallel Programming Library for Molecular Dynamics Simulations
A parallel programming library for molecular dynamics (MD) simulations is described and applied to the recently proposed split integration symplectic method (SISM) for MD simulation. The results show that for a system of 1024 linear chain molecules with an integration step of 4.5 fs parallel execution of SISM with the particle–particle interactions (PPIs) library on 32 computers gives efficienc...
متن کاملA Load Balanced Force-Domain Decomposition Algorithm for Parallel Molecular Dynamics Simulations
c © 2007 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher ment...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Computer Physics Communications
سال: 2017
ISSN: 0010-4655
DOI: 10.1016/j.cpc.2017.05.020