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 gains in sampling efficiency when the coupled–decoupled configurational-bias MC (CD–CBMC) algorithm is used compared with simulations using a single unbiased random trial position. Simulations using CD–CBMC reach equilibrium with 25 times fewer cycles than simulations using a single unbiased random trial position, with a small increase in computational cost. In a more challenging application, hybrid grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to hydrate a buried binding pocket in bovine pancreatic trypsin inhibitor. Water occupancies produced by GCMC/MD simulations are in close agreement with crystallographically identified positions, and GCMC/MD simulations have a computational efficiency that is 5 times better than MD simulations. py-MCMD is available on GitHub at .

MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC

“…As highlighted in some of the examples that follow, it can be computationally advantageous to utilize NAMD to quickly equilibrate the system using MD and then perform the desired MC simulations using GOMC. MoSDeF-GOMC can also build PDB, PSF, and parameter files for py-MCMD, − another Python software that utilizes both NAMD and GOMC to perform hybrid MD/MC simulations. However, unlike standard GOMC simulations, py-MCMD requires custom GOMC and NAMD control files that the user must modify outside of the MoSDeF-GOMC framework.…”

The Relationship between Structure and Performance of Different Polyimides Based on Molecular Simulations

“…With the development of computer technology and simulation software, simulation technology has been shown to greatly reduce the cost of material development and improve work efficiency [ 21 , 22 , 23 , 24 , 25 , 26 ]. A molecular dynamic simulation optimization experiment showed that an efficiency ratio of running time that tended to balance judgment achieved the highest value of 36.96% [ 27 ].…”

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

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