Journal
BIOPHYSICAL JOURNAL
Volume 108, Issue 8, Pages 1843-1847Publisher
CELL PRESS
DOI: 10.1016/j.bpj.2015.03.023
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Funding
- University of Warsaw [ICM/KDM/G31-4]
- National Science Centre [DEC-2011/03/N/NZ2/02482, DEC-2012/05/B/NZ1/00035]
- Ministry of Science and Higher Education
- HPC Infrastructure for Grand Challenges of Science and Engineering POWIEW project
- European Regional Development Fund
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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.
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