Chris, Thank you, that appears to be the issue then.
Running them again now with couple-intramol = yes Will report back once that is completed with the results. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Christopher Neale > Sent: Thursday, 17 October 2013 2:15 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] Gibbs Energy Calculation and charges > > Ah, I see. I guess that you are using couple-intramol = no (the default > in v4.6.3 at least). That means > that the intramolecular charge-charge interactions are always at full- > strength (and therefore different). > > I would expect that normal at lambda=0 should be the same as double at > lambda=0.5 only for > couple-intramol = yes > > If you were using couple-intramol = yes already, then I am as confused > as you are. > > Chris. > > -- original message -- > > You are correct in the first part of your statement, part that isn't > correct is I expect for the same charge on the atom I expect it to give > the same dH/dl value. > > For example, for the OE atom that I provided the graphs for ( > http://ozreef.org/stuff/octanol.gif and > http://ozreef.org/stuff/water.gif ) > > Lambda Normal > 0.0000 -0.5310 > Double > 0.0000 -1.0620 > 0.5000 -0.5310 > > Therefore, the normal charge molecule when lambda = 0 should be > identical to that double charge one when lambda = 0.5. They should be > the same in all manners, LJ, bonds, charges etc. > > So would I not expect to get the same dH/dl value out? > > Catch ya, > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
