[gmx-users] RE: Gibbs Energy Calculation and charges
Dallas.Warren at monash.edu
Thu Oct 17 04:58:15 CEST 2013
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 )
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?
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 12:24 PM
> To: gmx-users at 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
> 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
> 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.
> -- original message --
> Here is the molecule in octanol
> And here in water
> 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
> > making the charge disappear. One molecule has the normal charges, the
> > other all the charges are doubled. Taking the dHdl results for both
> > 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--
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