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Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications
Author(s) -
Bernardo Dan N.,
Ding Yanbo,
KroghJespersen Karsten,
Levy Ronald M.
Publication year - 1995
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.540160908
Subject(s) - computer science , inversion (geology) , parallel computing , dipole , computational science , flops , polarizability , distributed memory , shared memory , physics , quantum mechanics , molecule , paleontology , structural basin , biology
The efficient evaluation of polarizable molecular mechanics potentials on distributed memory parallel computers is discussed. The program executes at 7–10 Mflops/node on a 32‐node CM‐5 partition and is 19 times faster than comparable code running on a single‐processor HP 9000/735. On the parallel computer, matrix inversion becomes a practical alternative to the commonly used iterative method for the calculation of induced dipole moments. The former method is useful in cases such as free‐energy perturbation (FEP) simulations, which require highly accurate induced dipole moments. Matrix inversion is performed 110 times faster on the CM‐5 than on the HP. We show that the accuracy which is needed for FEP calculations with polarization can be obtained by either matrix inversion or by performing a large number of iteration cycles to satisfy convergence tolerances that are less than 10 −6 D. © 1995 by John Wiley & Sons, Inc.