Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 11, Issue 3, Pages 1077-1085Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct5009087
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Funding
- European Research Council under the European Union [306662]
- European Research Council (ERC) [306662] Funding Source: European Research Council (ERC)
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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.
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