Hi, On Wed, Mar 18, 2020 at 4:52 PM Johannes Hermann <johannes.herm...@tum.de> wrote:
> Dear all, > > I am calculating free energy changes with the alchemical free energy > framework provided in gromacs. My alchemical transformation involves a > charge change in a periodic system, where the periodicity is physical in > the bound state but "artificial" in the unbound state. I know there is a > bunch of literature dealing with correction schemes when using PME - but > it did not find anything when the periodicity is physical, e.g. when > simulating a membrane. So: > > What is the "error" in gromacs free energy calculation? Is it the > Interaction with itself in the periodic image or an interaction with a > changing neutralizing background charge which sums up? So should I try > keeping a zero net charge over all alchemical transition windows also in > the physical periodic setup. > > Yes that is always good to try to keep zero the net charge change Alessandra > Thanks and all the best > > Johannes > > -- > 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.
