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Free energy calculations in molecular simulations have a variety ofapplications including determining the strength of molecular processes such assolvation and binding. It has been recently shown that when removing the VDWand Coulomb potential terms of a group of atoms in a molecule by performing atransformation, the molecule can be treated as non interacting systems in thefree energy calculation. This treatment is applicable both when the molecule isin vacuum and in liquid and enables a very simple calculation of the freeenergies associated with the potentials that depend on the relative sphericalcoordinates of these atoms. Here we demonstrate the method in the free energycalculation of a Methanethiol molecule and compare the results to theseobtained by MD simulations in vacuum and in water. The comparison showsagreement between the results and faster computation when using the method byfactors varying between 5000 and 10^(12) for the same computational resources.

Free energy calculation of a molecule by removing VDW and Coulomb  interactions in a transformation and treating the molecule as non interacting  systems