Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 34, Issue 6, Pages 635-639Publisher
SPRINGER
DOI: 10.1007/s10822-020-00312-2
Keywords
SAMPL6; Binding free energy; Non-equilibrium; Crooks theorem; Double-system; single-box
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The alchemical nonequilibrium switching technique was one of several methods in the top tier of performance in the recent SAMPL6 SAMPLing challenge in both accuracy and efficiency. In this paper, in the context of nonequilibrium alchemical switching, we compare the efficiency of the double-system/single-box (DSSB) approach (used in the SAMPL6 challenges) to the standard single-system/double-box method (SSDB). Exploiting the Crooks theorem in a simple but effective test case, we analytically show that the DSSB approach is almost twice as efficient as SSDB for slow near-equilibrium switching but it gives basically no gain over the conventional SSDB approach when the variance of the work distribution exceeds few kBT with the potential of producing artifacts and entanglements if not judiciously implemented.
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