Good practices in free-energy calculations.

By Andrew Pohorille, Christopher Jarzynski, Christophe Chipot. Journal of Physical Chemistry B, 2010

586 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Statistical and Nonlinear Physics

View Paper: https://www.semanticscholar.org/paper/a94bb19ae342c22be319a19f7e90b674016ef24a

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In Atomic and Molecular Physics, and Optics

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Citations in the corpus

Colloquium : Statistical mechanics and thermodynamics at strong coupling: Quantum and classical (2019, methodology): “The direct use of the Jarzynski equality, in both numerical and real experiments, as a means of estimating the change of the free energy caused by a variation of a system’s parameter is known to often be severely hampered by statistical problems (Deng et al., 2017a,b; Kim et al., 2012; Lechner and D”
Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, background): “157 Following Jarzynski, 120 it is possible instead to define a protocol such that the perturbation is carried out over a certain amount of time in a fashion that disrupts the equilibrium.”
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].”
Guidelines for the analysis of free energy calculations (2015, methodology): “This resulted in the deterioration of the distribution overlap between states 4 and 6, which the ODM helps highlight: the ∆g i,i +1 function is not continuous and does not exhibit saw-like behavior over a substantial interval of the ∆U i,i − 1 values as it does in Fig.”
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask (2014, background): “Although much e ﬀ ort has been devoted in recent years to the characterization of errors that are associated with free-energy calculations, 7,8,72 − 81 estimating the reliability of such calculations remains an intricate task.”
Standard binding free energies from computer simulations: What is the best strategy? (2012, methodology): “As discussed in greater detail in the SI, the precision and accuracy of free-energy estimates are of different nature and sources, 71 thereby making their measure somewhat cumbersome and difficult to interpret.”