title: Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.
abstract: Modelling of conformational changes in biopolymers is one of the greatest challenges of molecular biophysics. Metadynamics is a recently introduced free energy modelling technique that enhances sampling of configurational (e.g. conformational) space within a molecular dynamics simulation. This enhancement is achieved by the addition of a history-dependent bias potential, which drives the system from previously visited regions. Discontinuous metadynamics in the space of essential dynamics eigenvectors (collective motions) has been proposed and tested in conformational change modelling. Here, we present an implementation of two continuous formulations of metadynamics in the essential subspace. The method was performed in a modified version of the molecular dynamics package GROMACS. These implementations were tested on conformational changes in cyclohexane, alanine dipeptide (terminally blocked alanine, Ace-Ala-Nme) and SH3 domain. The results illustrate that metadynamics in the space of essential coordinates can accurately model free energy surfaces associated with conformational changes.
authors.affiliation: Department of Structure and Function of Saccharides, Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 84538 Bratislava, Slovak Republic. chemspiw@savba.sk
authors.forename: Vojtech
authors.initials: V
authors.lastname: Spiwok
authors.forename: Blanka
authors.initials: B
authors.lastname: Králová
authors.forename: Igor
authors.initials: I
authors.lastname: Tvaroska
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D003198:Computer Simulation; D003510:Cyclohexanes / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry*; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation
chemical_list: D003510:Cyclohexanes; D004151:Dipeptides; C506365:Cyclohexane; D000409:Alanine