NE‐RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.27077
Abstract: 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… read more here.
Keywords: topology; relative dissociation; bidirectional nonequilibrium; protocol toolkit ... See more keywords
Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.1c00909
Abstract: We describe a step-by-step protocol for the computation of absolute dissociation free energy with GROMACS code and PLUMED library, which exploits a combination of advanced sampling techniques and nonequilibrium alchemical methodologies. The computational protocol has… read more here.
Keywords: dissociation free; free energy; virtual double; absolute dissociation ... See more keywords