Abstract
AbstractIn the context of the recent SAMPL6 SAMPLing challenge (Rizzi et al. 2020 in J Comput Aided Mol Des 34:601–633) aimed at assessing convergence properties and reproducibility of molecular dynamics binding free energy methodologies, we propose a simple explanation of the severe errors observed in the nonequilibrium switch double-system-single-box (NS-DSSB) approach when using unidirectional estimates. At the same time, we suggest a straightforward and minimal modification of the NS-DSSB protocol for obtaining reliable unidirectional estimates for the process where the ligand is decoupled in the bound state and recoupled in the bulk.
Funder
Università degli Studi di Firenze
Publisher
Springer Science and Business Media LLC
Subject
Physical and Theoretical Chemistry,Computer Science Applications,Drug Discovery
Cited by
5 articles.
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