[gmx-users] RE: Gibbs Energy Calculation and charges
Dallas.Warren at monash.edu
Thu Oct 17 06:31:48 CEST 2013
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.
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 Christopher Neale
> Sent: Thursday, 17 October 2013 2:15 PM
> To: gmx-users at 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.
> -- 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
> 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,
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