NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes.

BAR GROMACS HPC Jarzynski SAMPL challenges alchemical calculations molecular dynamics non-equilibrium relative free-energy calculations

Journal

Journal of computational chemistry

ISSN: 1096-987X

Titre abrégé: J Comput Chem

Pays: United States

ID NLM: 9878362

Informations de publication

Date de publication:
05 May 2023

Historique:

revised: 20 12 2022

received: 28 10 2022

accepted: 07 01 2023

pubmed: 28 1 2023

medline: 28 1 2023

entrez: 27 1 2023

Statut: ppublish

Résumé

We describe a step-by-step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention on the code and allows computing with good accuracy the RDFE between small molecules with arbitrary differences in volume, charge, and chemical topology. The procedure is illustrated for the challenging SAMPL9 batch of host-guest pairs. The article is supplemented by a detailed online tutorial, available at https://procacci.github.io/vdssb_gromacs/NE-RDFE and by a public Zenodo repository available at https://zenodo.org/record/6982932.

Identifiants

DOI: 10.1002/jcc.27077 PMID: 36704972

pubmed: 36704972

doi: 10.1002/jcc.27077

doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

Pagination

1221-1230

Subventions

Organisme : European Union - NextGenerationEU - CUP

ID : B83C22002830001

Informations de copyright

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