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231226s2023 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.27077
|2 doi
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|a eng
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|a Macchiagodena, Marina
|e verfasserin
|4 aut
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| 245 |
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|a NE-RDFE
|b A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes
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|c 2023
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|a Text
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|a ƒaComputermedien
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|a ƒa Online-Ressource
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|2 rdacarrier
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|a Date Completed 24.03.2023
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|a Date Revised 24.03.2023
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|a published: Print-Electronic
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|a Citation Status PubMed-not-MEDLINE
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|a © 2023 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.
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|a 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
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|a Journal Article
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|a BAR
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|a GROMACS
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|a HPC
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|a Jarzynski
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|a SAMPL challenges
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|a alchemical calculations
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|a molecular dynamics
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|a non-equilibrium
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|a relative free-energy calculations
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|a Pagliai, Marco
|e verfasserin
|4 aut
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|a Procacci, Piero
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 44(2023), 12 vom: 05. Mai, Seite 1221-1230
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnas
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|g volume:44
|g year:2023
|g number:12
|g day:05
|g month:05
|g pages:1221-1230
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|u http://dx.doi.org/10.1002/jcc.27077
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