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.
|Titolo:||Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering|
|Autori:||Gil-Ley, A.; Bussi, G.|
|Rivista:||JOURNAL OF CHEMICAL THEORY AND COMPUTATION|
|Data di pubblicazione:||2015|
|Digital Object Identifier (DOI):||10.1021/ct5009087|
|Fulltext via DOI:||10.1021/ct5009087|
|Appare nelle tipologie:||1.1 Journal article|