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 energy with GROMACS, based on a novel bidirectional
nonequilibrium alchemical approach.  The proposed methodology does not
require any intervention on the code and allows to compute 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 on the tutorial

https://procacci.github.io/vdssb_gromacs/NE-RDFE/