Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data.

ABSTRACT: Advances in biomolecular simulation methods and access to large scale computer resources have led to a massive increase in the amount of data generated. The key enablers have been optimization and parallelization of the simulation codes. However, much of the software used to analyze trajectory data from these simulations is still run in serial, or in some cases many threads via shared memory. Here, we describe the addition of multiple levels of parallel trajectory processing to the molecular dynamics simulation analysis software CPPTRAJ. In addition to the existing OpenMP shared-memory parallelism, CPPTRAJ now has two additional levels of message passing (MPI) parallelism involving both across-trajectory processing and across-ensemble processing. All three levels of parallelism can be simu

SUBMITTER: Roe DR 

PROVIDER: S-EPMC7313716 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature