Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.

ABSTRACT: Presented is the implementation of the Drude force field in the open-source OpenMM simulation package allowing for access to graphical processing unit (GPU) hardware. In the Drude model, electronic degrees of freedom are represented by negatively charged particles attached to their parent atoms via harmonic springs, such that extra computational overhead comes from these additional particles and virtual sites representing lone pairs on electronegative atoms, as well as the associated thermostat and integration algorithms. This leads to an approximately fourfold increase in computational demand over additive force fields. However, by making the Drude model accessible to consumer-grade desktop GPU hardware it will be possible to perform simulations of one microsecond or more in less than a m

SUBMITTER: Huang J 

PROVIDER: S-EPMC6031474 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature