Literature DB >> 32277315

A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge.

Piero Procacci1.   

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.

Entities:  

Keywords:  Binding free energy; Crooks theorem; Double-system/single-box; Non-equilibrium; SAMPL6

Year:  2020        PMID: 32277315     DOI: 10.1007/s10822-020-00312-2

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  4 in total

1.  Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.

Authors:  Zhiyi Wu; Philip C Biggin
Journal:  J Chem Theory Comput       Date:  2022-03-22       Impact factor: 6.578

2.  SAMPL7 blind predictions using nonequilibrium alchemical approaches.

Authors:  Piero Procacci; Guido Guarnieri
Journal:  J Comput Aided Mol Des       Date:  2021-01-04       Impact factor: 3.686

3.  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.

Authors:  Marina Macchiagodena; Marco Pagliai; Maurice Karrenbrock; Guido Guarnieri; Francesco Iannone; Piero Procacci
Journal:  J Chem Theory Comput       Date:  2020-10-22       Impact factor: 6.006

4.  Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS.

Authors:  Marina Macchiagodena; Maurice Karrenbrock; Marco Pagliai; Piero Procacci
Journal:  J Chem Inf Model       Date:  2021-11-01       Impact factor: 4.956

  4 in total

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