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Journal of Molecular Modeling

, 25:355 | Cite as

Enhanced GROMACS: toward a better numerical simulation framework

  • Hojjat Rakhshani
  • Effat DehghanianEmail author
  • Amin Rahati
Original Paper
  • 43 Downloads

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.

Keywords

GROMACS software package Metaheuristic optimization algorithms Molecular dynamic simulation Structure of proteins 

Notes

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.University of Upper AlsaceMulhouseFrance
  2. 2.Department of ChemistryUniversity of Sistan and BaluchestanZahedanIran
  3. 3.Department of Computer ScienceUniversity of Sistan and BaluchestanZahedanIran

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