Itoh SG, Okumura H. Replica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method.
J Chem Theory Comput 2012;
9:570-81. [PMID:
26589055 DOI:
10.1021/ct3007919]
[Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM). In RPM, not only exchanges between two replicas but also permutations among more than two replicas are performed. Furthermore, instead of the Metropolis algorithm, the Suwa-Todo algorithm is employed for replica-permutation trials to minimize its rejection ratio. We applied RPM to particles in a double-well potential energy, Met-enkephalin in a vacuum, and a C-peptide analog of ribonuclease A in explicit water. For comparison purposes, replica-exchange molecular dynamics simulations were also performed. As a result, RPM sampled not only the temperature space but also the conformational space more efficiently than REM for all systems. From our simulations of C-peptide, we obtained the α-helix structure with salt bridges between Gly2 and Arg10, which is known in experiments. Calculating its free-energy landscape, the folding pathway was revealed from an extended structure to the α-helix structure with the salt bridges. We found that the folding pathway consists of the two steps: The first step is the "salt-bridge formation step," and the second step is the "α-helix formation step."
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