[gmx-users] how to manipulate solute-solvent interactions in ff to get the correct solvation free energy?

[Justin Lemkul]

On 4/24/14, 3:48 PM, Golshan Hejazi wrote:
> Dear all,
>
> I have computed the solvation free energy of a molecule in a non aqueous solvent using thermodynamics integration in gromacs. The value is negative and high (-70kj/mol). The experimental value is almost -52kj/mol.
>
>  From the output of TI, there exist a lambda value which correspond to ~-53kj/mol and I would like to manipulate the force field parameters for the interaction between molecule and solute in order to get the right solvation free energy!
>
> Is it possible to do it in gromacs?

Well, it's certainly possible to scale the parameters as a function of lambda; 
all the equations for doing it are in the manual.  Whether or not the charges 
work out to be something physical is another issue.  At that point, you'd also 
need to introduce new atom types for each of those atoms with the new LJ 
parameters.  You'd also likely need to demonstrate that such a manipulation is 
valid within the context of the other species in the force field.  What is the 
source of the original topology that produced the -70 kJ/mol hydration free energy?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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