Exploiting the parallelisation inherent in the windowing approach to Monte Carlo energy perturbation calculations

A parallel version of a Monte Carlo free energy difference code has been implemented to exploit the potential for parallelisation inherent in the free energy perturbation windowing procedure. Since all the windows are run in parallel, the major overhead compared with the serial implementation is the requirement to increase the equilibration for each window from 10(6) configurations to 3 x 10(6) configurations (10(6) configurations were used for data collection for each window). For the perturbation of nitroimidazoles to their radical anions in a box of 500 water molecules, the parallel code gives essentially identical free energy of hydration differences to the serial code. The 64 processor GRAY T3D version of the code has an execution overhead of only 25% compared with the single processor version, suggesting that this approach has great potential. In particular, the approach could be combined with approaches to parallelise the non-bonded interactions, permitting parallelisation over several thousand processors. (C) 1998 Elsevier Science B.V.