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Biophys J. 2015 Apr 21;108(8):1843-7. doi: 10.1016/j.bpj.2015.03.023.

RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models.

Author information

1
Centre of New Technologies, University of Warsaw, Warsaw, Poland; Department of Chemistry, University of Warsaw, Warsaw, Poland. Electronic address: f.leonarski@cent.uw.edu.pl.
2
Centre of New Technologies, University of Warsaw, Warsaw, Poland. Electronic address: joanna@cent.uw.edu.pl.

Abstract

Coarse-grained (CG) models in molecular dynamics (MD) are powerful tools to simulate the dynamics of large biomolecular systems on micro- to millisecond timescales. However, the CG model, potential energy terms, and parameters are typically not transferable between different molecules and problems. So parameterizing CG force fields, which is both tedious and time-consuming, is often necessary. We present RedMDStream, a software for developing, testing, and simulating biomolecules with CG MD models. Development includes an automatic procedure for the optimization of potential energy parameters based on metaheuristic methods. As an example we describe the parameterization of a simple CG MD model of an RNA hairpin.

PMID:
25902423
PMCID:
PMC4407251
DOI:
10.1016/j.bpj.2015.03.023
[Indexed for MEDLINE]
Free PMC Article

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