[gmx-users] RE: Gibbs Energy Calculation and charges

Dallas Warren Dallas.Warren at monash.edu
Thu Oct 17 02:30:38 CEST 2013

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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