Chris, 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, 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 12:24 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] Gibbs Energy Calculation and charges > > 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 -- 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
