[gmx-users] RE: Gibbs Energy Calculation and charges
Dallas.Warren at monash.edu
Tue Oct 22 05:49:29 CEST 2013
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:
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)
Anyone with some insight on what is going on here?
>From the manual:
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.
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.
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 3:32 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] RE: Gibbs Energy Calculation and charges
> 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.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
> > in v4.6.3 at least). That means
> > that the intramolecular charge-charge interactions are always at
> > strength (and therefore different).
> > I would expect that normal at lambda=0 should be the same as double
> > lambda=0.5 only for
> > couple-intramol = yes
> > If you were using couple-intramol = yes already, then I am as
> > 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
> > 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
> > 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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