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The calculation of free-energy differences by constrained molecular-dynamics simulations
Abstract
In this paper we set out to derive a relation between the constraint force and the derivative of the free energy for a system in which only the reaction coordinate is constrained. Our result differs from the expression by Mülders et al. [J. Chem. Phys. 104, 4869 (1996)] because we take into account the effect of the constraint on the sampled phase-space distribution. The method is illustrated with two prototypical numerical examples.
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Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
Adaptive biasing force method for scalar and vector free energy calculations
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Metadata
- Authors
- den Otter, W. K., & Briels, W. J.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 1998-09-15
- Volume
- 109
- Issue
- 11
- Pages
- 4139-4146
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2112133710
- Cited by
- 183
- References
- 0
- FWCI
- 4.42
- Type
- journal article
- Language
- en
- Open access
- closed
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- den Otter, W. K., & Briels, W. J. (1998). The calculation of free-energy differences by constrained molecular-dynamics simulations. The Journal of Chemical Physics. https://doi.org/10.1063/1.477019
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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.
