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Vectorizing a general purpose molecular dynamics simulation program
Author(s) -
Teleman Olle,
Jönsson Bo
Publication year - 1986
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.540070108
Subject(s) - molecular dynamics , intramolecular force , covalent bond , degrees of freedom (physics and chemistry) , computer science , dynamics (music) , cutoff , aqueous solution , code (set theory) , minor (academic) , computational science , chemistry , computational chemistry , physics , thermodynamics , quantum mechanics , organic chemistry , set (abstract data type) , acoustics , political science , stereochemistry , law , programming language
A molecular dynamics program for arbitrary molecular mixtures is presented. All intramolecular degrees of freedom are treated explicitly, which means that the program is based on central forces only. A double time step technique has been devised in order to separate rapidly varying, covalent forces from slowly varying ones. Typically, the ratio between the different time steps is about 10, with only a minor computational effort spent in the evaluation of the covalent forces. The program source code is arranged so as to obtain maximal efficiency on a vector processor, while still being portable. On a Cray 1A, a typical simulation of an ion‐chelate in aqueous solution with 984 atoms requires a total of 29 μs/interaction with a spherical cutoff distance of 10Å.