> > somewhat off-topic but I wonder why in your free energy protocol you > only vary the vdW and electrostatic lambdas. What about the others? > Your mutation also transforms bonded terms and masses. >
Minor point - if you are taking the difference between two mutations (say, with and without a ligand), then it's better to leave the masses untouched -- any contribution will cancel. There are some weird issues with changing masses in the constraint terms and their contribution to the free energies that need to be accounted for post-hoc. -- 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.
