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Multidimensional replica-exchange method for free-energy calculations
Open accessAbstract
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.
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Cites
Equation of State Calculations by Fast Computing Machines
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953) · The Journal of Chemical Physics · doi:10.1063/1.1699114 · Cited by 37,192
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Parallel tempering: Theory, applications, and new perspectives
Earl, D. J., & Deem, M. W. (2005) · Physical Chemistry Chemical Physics · doi:10.1039/b509983h · Cited by 1,313
Using collective variables to drive molecular dynamics simulations
Fiorin, G., Klein, M. L., & Hénin, J. (2013) · Molecular Physics · doi:10.1080/00268976.2013.813594 · Cited by 1,053
Molecular Dynamics Simulations of Membrane Permeability
Venable, R. M., Krämer, A., & Pastor, R. W. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00486 · Cited by 394
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
Lopes, P. E. M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., & MacKerell, A. D. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400781b · Cited by 386
Metadata
- Authors
- Sugita, Y., Kitao, A., & Okamoto, Y.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2000-10-15
- Volume
- 113
- Issue
- 15
- Pages
- 6042-6051
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2074140794
- Cited by
- 827
- References
- 1
- FWCI
- 7.64
- Type
- journal article
- Language
- en
- Open access
- green
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- Sugita, Y., Kitao, A., & Okamoto, Y. (2000). Multidimensional replica-exchange method for free-energy calculations. The Journal of Chemical Physics. https://doi.org/10.1063/1.1308516
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
