Discovering free energy basins for macromolecular systems via guided multiscale simulation.

ABSTRACT: An approach for the automated discovery of low free energy states of macromolecular systems is presented. The method does not involve delineating the entire free energy landscape but proceeds in a sequential free energy minimizing state discovery; i.e., it first discovers one low free energy state and then automatically seeks a distinct neighboring one. These states and the associated ensembles of atomistic configurations are characterized by coarse-grained variables capturing the large-scale structure of the system. A key facet of our approach is the identification of such coarse-grained variables. Evolution of these variables is governed by Langevin dynamics driven by thermal-average forces and mediated by diffusivities, both of which are constructed by an ensemble of short molecular dyn

SUBMITTER: Sereda YV 

PROVIDER: S-EPMC3408247 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature