Paper Citing NAMD - Abstract
Leonarski, Filip; Trovato, Fabio; Tozzini, Valentina; Les, Andrzej; Trylska, Joanna
Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:4874-4889, NOV 2013
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.
