title: Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field.
abstract: 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.
authors.affiliation: Centre of New Technologies, University of Warsaw , Żwirki i Wigury 93, Warsaw 02-089, Poland.|Faculty of Chemistry, University of Warsaw , Pasteura 1, Warsaw 02-093, Poland.
authors.forename: Filip
authors.initials: F
authors.lastname: Leonarski
authors.affiliation: NEST, Istituto Nanoscienze - Cnr, Scuola Normale Superiore and Center of Nanotechnology and Innovation, IIT, Piazza San Silvestro 12, 56127 Pisa, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Trovato
authors.affiliation: NEST, Istituto Nanoscienze - Cnr and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Tozzini
authors.affiliation: Faculty of Chemistry, University of Warsaw , Pasteura 1, Warsaw 02-093, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Leś
authors.affiliation: Centre of New Technologies, University of Warsaw , Żwirki i Wigury 93, Warsaw 02-089, Poland.
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska