title: Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module.
abstract: We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte-Carlo/molecular dynamics (MD) simulations in the grand-canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand-canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand-canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand-canonical scheme is only minimal.
authors.affiliation: Centre for Integrative Bioinformatics Vrije Universiteit (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands; Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands. r.pool@vu.nl.
authors.forename: René
authors.initials: R
authors.lastname: Pool
authors.forename: Jaap
authors.initials: J
authors.lastname: Heringa
authors.forename: Martin
authors.initials: M
authors.lastname: Hoefling
authors.forename: Roland
authors.initials: R
authors.lastname: Schulz
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
authors.forename: K Anton
authors.initials: KA
authors.lastname: Feenstra
mesh_terms: D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D012984:Software