Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.

ABSTRACT: We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the algorithms that are used to exploit the processing power of the GPUs and show the performance that can be achieved in comparison to simulations on conventional CPU clusters. The implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (SPDP), or everything is computed in single precision (SPSP) or double precision (DPDP). In addition to performance, we have focused on understanding the implications of the different precision

SUBMITTER: Gotz AW 

PROVIDER: S-EPMC3348677 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature