ArticleJournal of computer-aided molecular design2020
A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge.
Article in Journal of computer-aided molecular design, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.Journal of chemical theory and computation · 2022Article
- Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS.Journal of chemical information and modeling · 2021Article
- SAMPL7 blind predictions using nonequilibrium alchemical approaches.Journal of computer-aided molecular design · 2021Article
- Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease.Journal of chemical theory and computation · 2020Article
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Abstract
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 [Formula: see text], with the potential of producing artifacts and entanglements if not judiciously implemented.
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