Dear Dallas: Am I correct that you are saying that for both the regular-charge and double-charge solute molecule, you decoupled the solvent-solute charge-charge interactions and expected that the dH/dL and overall free energy values of the double-charge solute would be exactly two times the respective values of the regular-charge system?
For that to be true, I believe it would also have to be true that doubling the charges has no bearing on the conformations that are sampled (including the solvent), which is certainly incorrect. To clarify my point, I believe that if you used the conformations from the regular-charge simulations in an mdrun -rerun using the double-charge topology (assuming that such a thing is even possible), then I do agree that you would expect exactly double the magnitudes for the free energy. But if doubling the charge affects solute or solvent conformation, then I would expect that the exact relationship is generally impossible to predict a priori. Chris. -- original message -- Here is the molecule in octanol http://ozreef.org/stuff/octanol.gif And here in water http://ozreef.org/stuff/water.gif Just realised, it is actually quite different in water, consistently. So the only difference between the two simulations is the charges on the molecule have been multiplied by 2. Same settings, same bonded and LJ topology etc. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.warren at 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-bounces at gromacs.org [mailto:gmx-users- > bounces at gromacs.org] On Behalf Of Dallas Warren > Sent: Thursday, 17 October 2013 9:06 AM > To: Discussion list for GROMACS users > Subject: [gmx-users] Gibbs Energy Calculation and charges > > We have a molecule, and have run two sets of Gibbs energy calculation, > making the charge disappear. One molecule has the normal charges, the > other all the charges are doubled. Taking the dHdl results for both and > plotting against the charge of a selected atom (charge based at each > lambda value) should those results over lap? > > I thought that they would, since charge only is being changed, and it > is a linear function of lambda. However, are getting some deviation > closer to the lambda=0 values for the normal charge, it is lower than > the double charged molecule around lambda = 0.5 > > Can provide graphs etc when I am back at my workstation. > > Any suggestions on whether should be over lapping or what we may be > doing incorrectly? > > Catch ya, > > Dallas Warren-- -- 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
