On Tue, 19 May 2015 12:03:41 -0400 Michael Shirts <mrshi...@gmail.com> wrote:
> Yep, that's what I generally do. Almost all alchemical changes > involve a difference in two calculations (since the alchemical change > itself is unphysical). Even one-calculation solvation free energy > calculations are actually calculating the difference in free energy > from liquid to vapor state. This reminds me: there was recently a discussion around couple-moltype on this list. My understanding is that this can be used for "absolute" free energies. But what I really want to make sure is this: as far as I can see in the code and I think the manual says that too is that when couple-moltype is not set in the .mdp none of the other couple- parameters have any effect should I set any of the to something. Do I get this right? Many thanks for the answers, Hannes. > On Tue, May 19, 2015 at 11:58 AM, Hannes Loeffler < > hannes.loeff...@stfc.ac.uk> wrote: > > > On Tue, 19 May 2015 11:37:11 -0400 > > Michael Shirts <mrshi...@gmail.com> wrote: > > > > > > > > > > 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. > > > > So you suggest to leave the mass lambdas simply at their initial (or > > final) value to be safe in case constraints are involved (and I am > > too lazy to check)? > > -- > > 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. > > -- 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.