This archive contains all input files needed to run the molecular dynamics simulations for solvation free energy calculations using GROMACS. These include the topologies ("system.top"), initial configurations ("conf_*.gro"), input control files ("prod*.mdp") and run scripts ("run*.sh). It also contains a Perl script used to analyse the output data from GROMACS ("run_analysis.pl"), producing a Hamiltonian gradient profile suitable for numerical integration. The data is organised first by molecular model, then by solute/solvent pair, according to Table S7 of the corresponding paper. The data has never been made public before.