DOI: 10.1063/1.1590311. Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

10.1063/1.1590311

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

Jarzynski’s equality is applied to free energy calculations from steered molecular dynamics simulations of biomolecules. The helix-coil transition of deca-alanine in vacuum is used as an example. With about ten trajectories sampled, the second order cumulant expansion, among the various averaging schemes examined, yields the most accurate estimates. We compare umbrella sampling and the present method, and find that their efficiencies are comparable.

Bibliography

Park, S., Khalili-Araghi, F., Tajkhorshid, E., & Schulten, K. (2003). Free energy calculation from steered molecular dynamics simulations using Jarzynskiâs equality. The Journal of Chemical Physics, 119(6), 3559â3566.

Authors 4

Sanghyun Park (first)
Fatemeh Khalili-Araghi (additional)
Emad Tajkhorshid (additional)
Klaus Schulten (additional)

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Dates

Type	When
Created	22 years, 1 month ago (July 24, 2003, 6:30 p.m.)
Deposited	1 year, 6 months ago (Feb. 5, 2024, 6:10 p.m.)
Indexed	1 day, 5 hours ago (Aug. 29, 2025, 6:42 a.m.)
Issued	22 years ago (Aug. 8, 2003)
Published	22 years ago (Aug. 8, 2003)
Published Print	22 years ago (Aug. 8, 2003)

Funders 0

None

BibTeX

@article{Park_2003, title={Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality}, volume={119}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.1590311}, DOI={10.1063/1.1590311}, number={6}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Park, Sanghyun and Khalili-Araghi, Fatemeh and Tajkhorshid, Emad and Schulten, Klaus}, year={2003}, month=aug, pages={3559–3566} }

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