Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

ABSTRACT: The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute

SUBMITTER: Harger M 

PROVIDER: S-EPMC5539969 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature