title: RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models.
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.
authors.affiliation: 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.
authors.forename: Filip
authors.initials: F
authors.lastname: Leonarski
authors.affiliation: Centre of New Technologies, University of Warsaw, Warsaw, Poland. Electronic address: joanna@cent.uw.edu.pl.
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012984:Software
chemical_list: D004247:DNA