Py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.

ABSTRACT: py-MCMD, an open-source Python software, provides a robust workflow layer that manages communication of relevant system information between the simulation engines NAMD and GOMC and generates coherent thermodynamic properties and trajectories for analysis. To validate the workflow and highlight its capabilities, hybrid Monte Carlo/molecular dynamics (MC/MD) simulations are performed for SPC/E water in the isobaric-isothermal (NPT) and grand canonical (GC) ensembles as well as with Gibbs ensemble Monte Carlo (GEMC). The hybrid MC/MD approach shows close agreement with reference MC simulations and has a computational efficiency that is 2 to 136 times greater than traditional Monte Carlo simulations. MC/MD simulations performed for water in a graphene slit pore illustrate significant ga

SUBMITTER: Barhaghi MS 

PROVIDER: S-EPMC9760104 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature