ReviewBiophysics and physicobiology2018
Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant.
Review in Biophysics and physicobiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method.Scientific reports · 2026Article
- Extended Conformational Selection in the Antigen-Antibody Interaction of the PfAMA1 Protein.The journal of physical chemistry. B · 2024Article
- myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.Biophysics and physicobiology · 2020Article
- Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.Computational and structural biotechnology journal · 2019Review
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3 authors.
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Abstract
The replica-exchange molecular dynamics (REMD) method has been used for conformational sampling of various biomolecular systems. To maximize sampling efficiency, some adjustable parameters must be optimized. Although it is agreed that shorter intervals between the replica-exchange attempts enhance traversals in the temperature space, details regarding the artifacts caused by these short intervals are controversial. In this study, we revisit this problem by performing REMD simulations on an alanine octapeptide in an implicit solvent. Fifty different sets of conditions, which are a combination of five replica-exchange periods, five different numbers of replicas, and two thermostat coupling time constants, were investigated. As a result, although short replica-exchange intervals enhanced the traversals in the temperature space, they led to artifacts in the ensemble average of the temperature, potential energy, and helix content. With extremely short replica-exchange intervals, i.e., attempted at every time step, the ensemble average of the temperature deviated from the thermostat temperature by
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