String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

ABSTRACT: The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (Stri

SUBMITTER: Branduardi D 

PROVIDER: S-EPMC3981481 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature