Convergence of single-step free energy perturbation
By S. Boresch, H. Woodcock. 2017
54 citations recorded by the source corpus.
ABSTRACT The convergence of free energy perturbation (Zwanzig's equation) and its non-equilibrium extension (Jarzynski's equation) is herein investigated from a practical point of view. We focus on cases where neither intermediate steps nor two-sided methods (Bennett, Crooks) can be used to compute the free energy difference of interest. Using model data sampled from several probability densities, as well as comparing results of actual free energy simulations with reference values, we find, in agreement with existing theoretical work, that systematic errors are strongly correlated with the variance in the distribution of energy differences / non-equilibrium work values. The bias metric Π introduced by Wu and Kofke (J. Chem. Phys. 121, 8742 (2004)) is found to be a useful test for the presence of bias, i.e. systematic error in the results. By contrast, use of the second-order cumulant approximation to approximate the full Zwanzig or Jarzynski equation leads to poorer results in almost all cases.
Subfields: Atmospheric Science, Atomic and Molecular Physics, and Optics, Statistical and Nonlinear Physics
View Paper: https://www.semanticscholar.org/paper/abb3e76c36293fda1779316fdf4dea59c6d7b75e
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In Atomic and Molecular Physics, and Optics
In Statistical and Nonlinear Physics
Citations in the corpus
- Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0] (2021, background): “Examples for these is one step perturbation [7, 122–125] or enveloping distribution sampling (EDS) [126–130].”
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.2] (2021, background): “Examples for these is one step perturbation [7, 122–125] or enveloping distribution sampling (EDS) [126–130].”