期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 9, 期 11, 页码 4874-4889出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct4005036
关键词
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资金
- ICM University of Warsaw [G31-4]
- National Science Center [DEC-2011/03/N/NZ2/02482, DEC-2012/05/B/NZ1/00035]
- Foundation for Polish Science [TEAM/2009-3/8]
- HPC Infrastructure for Grand Challenges of Science and Engineering POWIEW project
- European Regional Development Fund
Simulations using residue-scale coarse-grained models of biomolecules are less computationally demanding than simulations employing full-atomistic force fields. However, the coarse-grained models are often difficult and tedious to parametrize for certain applications. Therefore, a systematic and objective method to help develop or adapt the coarse-grained models is needed. We present an automatic method that implements an evolutionary algorithm to find a set of optimal force field parameters for a one-bead coarse-grained model. In addition to an optimized force field, parameter correlations and significance of the potential energy terms can be determined. The method is applied to two classes of problems: the dynamics of an RNA helix and the RNA structure prediction.
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