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Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

ABSTRACT: 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 strengths 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.

SUBMITTER: Gil-Ley A

PROVIDER: S-EPMC4364913 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

Gil-Ley Alejandro A Bussi Giovanni G

Journal of chemical theory and computation 20150301 3

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 strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are sig ...[more]

PMID: 25838811

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