Free energy level correction by Monte Carlo resampling with weighted histogram analysis method(dagger)

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Free energy calculations may provide vital information for studying various chemical and biological processes. Quantum mechanical methods are required to accurately describe interaction energies, but their computations are often too demanding for conformational sampling. As a remedy, level correction schemes that allow calculating high level free energies based on conformations from lower level simulations have been developed. Here, we present a variation of a Monte Carlo (MC) resampling approach in relation to the weighted histogram analysis method (WHAM). We show that our scheme can generate free energy surfaces that can practically converge to the exact one with sufficient sampling, and that it treats cases with insufficient sampling in a more stable manner than the conventional WHAM-based level correction scheme. It can also provide a guide for checking the uncertainty of the level-corrected surface and a well-defined criterion for deciding the extent of smoothing on the free energy surface for its visual improvement. We demonstrate these aspects by obtaining the free energy maps associated with the alanine dipeptide and proton transfer network of the KillerRed protein in explicit water, and exemplify that the MC resampled WHAM scheme can be a practical tool for producing free energy surfaces of realistic systems.
Publisher
CHINESE PHYSICAL SOC
Issue Date
2020-04
Language
English
Article Type
Article; Proceedings Paper
Citation

CHINESE JOURNAL OF CHEMICAL PHYSICS, v.33, no.2, pp.183 - 195

ISSN
1674-0068
DOI
10.1063/1674-0068/cjcp2001001
URI
http://hdl.handle.net/10203/275330
Appears in Collection
CH-Journal Papers(저널논문)
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