MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system.

ABSTRACT: We report an optimized version of the molecular dynamics program MOIL that runs on a shared memory system with OpenMP and exploits the power of a Graphics Processing Unit (GPU). The model is of heterogeneous computing system on a single node with several cores sharing the same memory and a GPU. This is a typical laboratory tool, which provides excellent performance at minimal cost. Besides performance, emphasis is made on accuracy and stability of the algorithm probed by energy conservation for explicit-solvent atomically-detailed-models. Especially for long simulations energy conservation is critical due to the phenomenon known as "energy drift" in which energy errors accumulate linearly as a function of simulation time. To achieve long time dynamics with acceptable accuracy the drift mus

SUBMITTER: Ruymgaart AP 

PROVIDER: S-EPMC3274753 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature