Just want this to make another pass, just in case those in the know missed it.
Using couple-intrmol = yes the resulting dH/dl plot actually looks like that at lamba = 1 it is actually equal to couple-intramol = no with lambda = 0. Should that be the case? 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 Dallas Warren > Sent: Tuesday, 22 October 2013 2:49 PM > To: Discussion list for GROMACS users > Subject: [gmx-users] RE: Gibbs Energy Calculation and charges > > I have completed the simulations using couple-intramol = yes > > Reminder, have a molecule that are calculating the Gibbs energy of > hydration and solvation (octanol). In one topology the only difference > is the atomic charges have been doubled. Considering that charges are > scaled linearly with lambda, the normal charge values of dH/dl from > lambda 0 to 1 obtained should reproduce that of the double charged > molecule from lambda 0.5 to 1.0. > > Here is the mdout.mdp file from one of the simulations using couple- > intramol = yes. The difference with the simulations run using couple- > intramol = no is only that setting, checked using the diff command. > Copy of the mdout.mdp file can be found: > > http://ozreef.org/stuff/gromacs/mdout.mdp > > Changing to couple-intrmol = yes makes things significantly worse. > > Here are the plots of dH/dl obtained as a function of the charge of one > of the atoms, OE (calculated based on fact that at lambda = 0 fully > charged, lambda = 1 no charged) > > http://ozreef.org/stuff/gromacs/couple-intramol.png > > Anyone with some insight on what is going on here? > > >From the manual: > ________________________ > couple-intramol: > > no > All intra-molecular non-bonded interactions for moleculetype > couple-moltype are replaced by exclusions and explicit pair > interactions. In this manner the decoupled state of the molecule > corresponds to the proper vacuum state without periodicity effects. > yes > The intra-molecular Van der Waals and Coulomb interactions are > also turned on/off. This can be useful for partitioning free-energies > of relatively large molecules, where the intra-molecular non-bonded > interactions might lead to kinetically trapped vacuum conformations. > The 1-4 pair interactions are not turned off. > ________________________ > > 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 Dallas Warren > > Sent: Thursday, 17 October 2013 3:32 PM > > To: Discussion list for GROMACS users > > Subject: [gmx-users] RE: Gibbs Energy Calculation and charges > > > > 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 > -- > 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
