On Tue, 16 May 2017 15:13:10 -0400 Dan Gil <dan.gil9...@gmail.com> wrote:
> If you do this via decoupling ("absolute" transformation) you do that > > once for molecule A and once for molecule B. > > > I believe you are referring to the BAR method? I am trying to see if > I get the same results as another group. They used thermodynamic > integration from A to B, so I decided to spend some more time with > this. I will try later if I get consistent results for both methods. No, I am not referring to a specific analysis methods. I commented on an alternative pathway. > transforming the masses may interact badly > > with bond constraints that are applied to alchemically transformed > > bonds > > > Thank you for this information! Do you know if there are there > publications that refer to this issue? Not that I know of. -- 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.