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Enhanced GROMACS: toward a better numerical simulation framework

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Abstract

The GROMACS software package represented a promising direction toward the molecular dynamic simulation and there is ongoing interest to extend it. In this study, we introduce a new component into the conventional package with the goal being to facilitate the process of finding the native structure of proteins with minimal free-energy value. We achieved this through incorporating a wide range of metaheuristic optimization algorithms and force fields, leading up to the EGROMACS molecular simulation toolkit. Compared with other programs, the EGROMACS supports all standard force fields as well as new minimization algorithms and Hybrid MPI/OpenMP parallelization. We applied the proposed EGROMACS framework to minimize the structure of several target sequences. The obtained results showed comparative performance of the introduced framework to current well-known molecular simulation algorithms. This extension to the GROMACS, however, uses metaheuristic algorithms to address the problem.

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Author information

Authors and Affiliations

  1. University of Upper Alsace, Mulhouse, France

    Hojjat Rakhshani

  2. Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran

    Effat Dehghanian

  3. Department of Computer Science, University of Sistan and Baluchestan, Zahedan, Iran

    Amin Rahati

Authors
  1. Hojjat Rakhshani
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  2. Effat Dehghanian
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  3. Amin Rahati
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Correspondence to Effat Dehghanian.

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Rakhshani, H., Dehghanian, E. & Rahati, A. Enhanced GROMACS: toward a better numerical simulation framework. J Mol Model 25, 355 (2019). https://doi.org/10.1007/s00894-019-4232-z

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  • DOI: https://doi.org/10.1007/s00894-019-4232-z

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