PLUMED Plugin Integration into High Performance Pmemd Program for Enhanced Molecular Dynamics Simulations

Viktor V. Drobot; Evgeny M. Kirilin; Kirill E. Kopylov; Vytas K. Švedas

doi:10.14529/jsfi210408

Authors

Viktor V. Drobot Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology
Evgeny M. Kirilin Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology
Kirill E. Kopylov Lomonosov Moscow State University, Research Computing Center
Vytas K. Švedas Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics

DOI:

https://doi.org/10.14529/jsfi210408

Keywords:

High performance pmemd program, enhanced molecular dynamics simulations, PLUMED plugin integration, metadynamics, CUDA, GPU

Abstract

Metadynamics as an enhanced sampling procedure of molecular dynamics simulations is an effective tool to simulate complex molecular motions, conformations and reactivity, including enzyme plasticity and catalysis. The classic non-enhanced molecular simulation tools have reached unprecedently high performance utilizing GPU units, however their implementation for enhanced sampling are still on demand. The widespread AMBER (molecular dynamics package) + PLUMED (metadynamics plugin) still does not take advantage of GPU computing or the CPU utilization optimization included in the AMBER pmemd program. In this work we have developed PLUMED binding to pmemd program resolving performance issues within hybrid molecular dynamics/metadynamics runs. Preliminary checks and test results of the model system have validated this implementation.

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