Relative binding free Energy calculations in GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes

We describe a step-by-step protocol for the computation of relative dissociation free energies with GROMACS, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention in the code. It allows computing with good accuracy the RBFE between small molecules with arbitrary differences in volume, charge, and Tanimoto index. The procedure is illustrated for the challenging SAMPL9 batch

Related Organizations

University of Florence
Italy

Keywords

Relative free energy calculations, Alchemical calculations, non-equilibrium, BAR, GROMACS, HPC, Jarzynski, SAMPL challenges, Molecular dynamics, Relative free energy calculations, Alchemical calculations, non-equilibrium, BAR, GROMACS, HPC, Jarzynski, SAMPL challenges, Molecular dynamics

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