Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module

Authors

  • René Pool,

    Corresponding author
    1. Centre for Integrative Bioinformatics Vrije Universiteit (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands
    2. Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands
    • Centre for Integrative Bioinformatics Vrije Universiteit (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands
    Search for more papers by this author
  • Jaap Heringa,

    1. Centre for Integrative Bioinformatics Vrije Universiteit (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands
    2. Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands
    Search for more papers by this author
  • Martin Hoefling,

    1. Department of Theoretical & Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
    Search for more papers by this author
  • Roland Schulz,

    1. University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, 1 Bethel Valley, Oak Ridge, Tennessee
    Search for more papers by this author
  • Jeremy C. Smith,

    1. University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, 1 Bethel Valley, Oak Ridge, Tennessee
    Search for more papers by this author
  • K. Anton Feenstra

    1. Centre for Integrative Bioinformatics Vrije Universiteit (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands
    2. Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands
    Search for more papers by this author

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. © 2012 Wiley Periodicals, Inc.

Ancillary