Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization.

ABSTRACT: We report Graphics Processing Unit (GPU) and Open-MP parallel implementations of water-specific force calculations and of bond constraints for use in Molecular Dynamics simulations. We focus on a typical laboratory computing-environment in which a CPU with a few cores is attached to a GPU. We discuss in detail the design of the code and we illustrate performance comparable to highly optimized codes such as GROMACS. Beside speed our code shows excellent energy conservation. Utilization of water-specific lists allows the efficient calculations of non-bonded interactions that include water molecules and results in a speed-up factor of more than 40 on the GPU compared to code optimized on a single CPU core for systems larger than 20,000 atoms. This is up four-fold from a factor of 10 reported

SUBMITTER: Ruymgaart AP 

PROVIDER: S-EPMC3524996 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature