Computation of Solvation Free Energies by Expanded Ensemble

Expanded Ensemles is a methodology for computation of free energies, for details see papers listed here. MDynaMix v. 5.2 and higher fully implements the expanded ensemble method for computation of free energy change during transfer of one or more molecules from an ideal gas phase to the solvent. Starting from v.5.2.5, the algorithm implements soft-core potential reaction path while inserting solute to the system. The example presented here contains input and output files for computation of solvation free energy of a neutral lidocaine molecule in water. The resulting solvation free energy is defined as -31.5 +/- 0.9 kJ/mol).

The system:

MDynaMix files:

Structure-Force Field file for lidocaine: lidocaine.mmol

Structure-Force Field file for water: H2O.mmol

MDynamix input file: lidocaine.in

MDynamix output file: lidocaine.out (soft core potentals)