A rapid method for determining rate constants by molecular dynamics
Abstract
A simple method is presented for determining rate constants in activated barrier crossing in a computer simulation. Instead of calculating the reactive flux, this method focuses on dynamics in the system with an absorbing barrier placed at the transition state. This method leads to a large reduction in CPU time for the low and high friction regimes.
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Rate constants can be derived from molecular dynamics, as reported for individual reactions and for reaction networks.
“Molecular dynamics-based GARD is envisaged, among other directions, as involving network kinetics simulations, in which the rate constants are derived from molecular dynamics, as reported for individual reactions [260,265,266], as well as for reaction networks [267].”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [266]
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Reaction-rate theory: fifty years after Kramers
Hänggi, P., Talkner, P., & Borkovec, M. (1990) · Reviews of Modern Physics · doi:10.1103/revmodphys.62.251 · Cited by 6,154 · see citing works
Systems protobiology: origin of life in lipid catalytic networks
Lancet, D., Zidovetzki, R., & Markovitch, O. (2018) · Journal of The Royal Society Interface · doi:10.1098/rsif.2018.0159 · Cited by 182 · see citing works
- Authors
- Straub, J. E., & Berne, B. J.
- Affiliations
- Columbia University (US)
- ORCID
- Straub, John E.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 1985-08-01
- Volume
- 83
- Issue
- 3
- Pages
- 1138-1139
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2068415757
- Cited by
- 58
- References
- 0
- Citations by year
- 2025: 1 · 2018: 3 · 2016: 2 · 2012: 1
- FWCI
- 5.94
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The Journal of Chemical Physics (publishedVersion)
- Topics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Physical Sciences › Physics and Astronomy › Condensed Matter Physics › Theoretical and Computational Physics
- Keywords
- rate constants, absorbing barriers, transition state, reactive flux, reaction rate calculation, CPU time reduction, molecular dynamics
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