Predicting Hydrophobic Solvation by Molecular Simulation: 2. New United-atom Model for Alkanes, Alkenes and Alkynes

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 class of compound, then by solute/solvent pair, according to Table S5 of the corresponding paper. The data has never been made public before.