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Multidimensional free‐energy calculations using the weighted histogram analysis method
Abstract
The recently formulated weighted histogram analysis method (WHAM)1 is an extension of Ferrenberg and Swendsen's multiple histogram technique for free‐energy and potential of mean force calculations. As an illustration of the method, we have calculated the two‐dimensional potential of mean force surface of the dihedrals gamma and chi in deoxyadenosine with Monte Carlo simulations using the all‐atom and united‐atom representation of the AMBER force fields. This also demonstrates one of the major advantages of WHAM over umbrella sampling techniques. The method also provides an analysis of the statistical accuracy of the potential of mean force as well as a guide to the most efficient use of additional simulations to minimize errors. © 1995 John Wiley & Sons, Inc.
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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
Cited by
Laio, A., & Gervasio, F. L. (2008) · Reports on Progress in Physics · doi:10.1088/0034-4885/71/12/126601 · Cited by 1,619
Assessing the Accuracy of Metadynamics
Laio, A., Rodriguez-Fortea, A., Gervasio, F. L., Ceccarelli, M., & Parrinello, M. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045424k · Cited by 517
Flexible Docking in Solution Using Metadynamics
Gervasio, F. L., Laio, A., & Parrinello, M. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0445950 · Cited by 287
Using AMBER18 for Relative Free Energy Calculations
Song, L. F., Lee, T.-S., Zhu, C., York, D. M., & Merz, K. M. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00105 · Cited by 234
Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy
Mendes de Oliveira, D., Zukowski, S. R., Palivec, V., Hénin, J., Martinez-Seara, H., Ben-Amotz, D., Jungwirth, P., & Duboué-Dijon, E. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp02987d · Cited by 73
Metadata
- Authors
- Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 1995-11
- Volume
- 16
- Issue
- 11
- Pages
- 1339-1350
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2059844062
- Cited by
- 866
- References
- 1
- FWCI
- 3.45
- Type
- journal article
- Language
- en
- Open access
- closed
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- Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1995). Multidimensional free‐energy calculations using the weighted histogram analysis method. Journal of Computational Chemistry. https://doi.org/10.1002/jcc.540161104
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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