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OOPSE: An object‐oriented parallel simulation engine for molecular dynamics
Author(s) -
Meineke Matthew A.,
Vardeman Charles F.,
Lin Teng,
Fennell Christopher J.,
Gezelter J. Daniel
Publication year - 2005
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20161
Subject(s) - quaternion , molecular dynamics , verlet integration , integrator , computer science , atom (system on chip) , simple (philosophy) , code (set theory) , dipole , point (geometry) , degrees of freedom (physics and chemistry) , dynamics (music) , decomposition , computational science , computational chemistry , chemistry , physics , mathematics , parallel computing , thermodynamics , programming language , quantum mechanics , geometry , computer network , philosophy , set (abstract data type) , bandwidth (computing) , epistemology , organic chemistry , acoustics
OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. “sticky” atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force‐based decomposition method. Simulations are specified using a very simple C‐based meta‐data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion‐based schemes. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 252–271, 2005