Vectorizing a general purpose molecular dynamics simulation program

Abstract

AbstractA 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.