Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications

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.