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

By Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, Klaus Schulten. 2003

726 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology

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In Atomic and Molecular Physics, and Optics

In Molecular Biology

Citations in the corpus

Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “Nevertheless, variants of the Jarzynski identity have been successfully applied to rare examples of sufficiently fast-relaxing systems [83].”
Stochastic thermodynamics, fluctuation theorems and molecular machines (2012, background): “Some of the papers dealing with this issue are [86, 137, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480].”
QM/MM Methods for Biological Systems (2006, background): “This relation has become the foundation for “fast-growth” [351] or “multiple-steering” [349, 352, 353] simulations, in which irreversible-work values from deliberately non-adiabatic switching processes are accumulated and exponentially averaged according to Eq.”
Scalable molecular dynamics with NAMD (2005, methodology): “Application of the Jarzynski identity (19) is comparable in efficiency to the umbrella sampling method [81].”
Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, background): “144,145 Much effort has been invested to address this reweighting problem in aMD.”
Nonequilibrium fluctuations in small systems: From physics to biology (2007, methodology): “Free-energy recovery techniques are also used in numerical simulations to evaluate free-energy differences [105, 106, 107, 108] and reconstruct free-energy profiles or potentials of mean-field force [109, 110].”