Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field

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• 作者：Filip Leonarski ; Fabio Trovato ; Valentina Tozzini ; Andrzej Le艣 ; Joanna Trylska
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2013
• 出版时间：November 12, 2013
• 年：2013
• 卷：9
• 期：11
• 页码：4874-4889
• 全文大小：950K
• 年卷期：v.9,no.11(November 12, 2013)
• ISSN：1549-9626

文摘

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.