[gmx-users] Gibbs Energy Calculation and charges

Christopher Neale chris.neale at mail.utoronto.ca
Thu Oct 17 03:24:16 CEST 2013

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.


-- 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 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--

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