Dear all, I am trying to calculate relative free energies of hydration between two similar molecules. I want to do the following things:
(1) Totally remove the VDW and Coulomb interactions of few atoms (remove their interaction with all atoms). (2) Transform the Coulomb term (partial charge) of few atoms to a certain value (such that this value will be the one relevant for the interactions with all the other atoms). If I understand correctly the (1) transformation can be implemented by turning the charges to zero in state B and further changing it to DUM atoms by another transformation. Could you please advise if the (2) option can be implemented through Gromacs free energy mdp options?. And what should be the "coupl-intramol" value to be used during these transformations (I do not want to decouple solute-solvent interaction during these transformations). Thanks in advance. -- *-------------------- Regards,Bipin Singh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.