GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

ABSTRACT:

Motivation

Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources.

Results

Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to

SUBMITTER: Pronk S 

PROVIDER: S-EPMC3605599 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature