The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.
Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering / Gil Ley, Alejandro; Bussi, Giovanni. - In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. - ISSN 1549-9618. - 11:3(2015), pp. 1077-1085. [10.1021/ct5009087]
|Titolo:||Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering|
|Autori:||Gil Ley, Alejandro; Bussi, Giovanni|
|Data di pubblicazione:||2015|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1021/ct5009087|
|Fulltext via DOI:||http://dx.doi.org/10.1021/ct5009087|
|Appare nelle tipologie:||1.1 Journal article|