A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

ABSTRACT: With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simul

SUBMITTER: Purawat S 

PROVIDER: S-EPMC5479118 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature