Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism.

ABSTRACT: In this work a new method for the automatic exploration and calculation of multidimensional free energy landscapes is proposed. Inspired by metadynamics, it uses several collective variables that are relevant for the investigated process and a bias potential that discourages the sampling of already visited configurations. The latter potential allows escaping a local free energy minimum following the direction of slow motions. This is different from metadynamics in which there is no specific direction of the biasing force and the computational effort increases significantly with the number of collective variables. The method is tested on the Ace-Ala3-Nme peptide, and then it is applied to investigate the Trp-cage folding mechanism. For this protein, within a few hundreds of nanoseconds, a b

SUBMITTER: Marinelli F 

PROVIDER: S-EPMC3817379 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature