I think the grammar got a little garbled there, so I'm not sure quite what you are claiming.
One important thing to remember; 1-4 interactions are treated as bonded interactions right now FOR COUPLE intramol (not for lambda dependence of the potential energy function), so whether couple-intramol is set to yes or no does not affect these interactions at all. It only affects the nonbondeds with distances greater than 1-5. At least to me, this is nonintuitive (and we're coming up with a better scheme for 5.0), but might that explain what you are getting? On Tue, Oct 29, 2013 at 9:44 PM, Dallas Warren <dallas.war...@monash.edu> wrote: > 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? 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