[gmx-users] need help with free energy of solvation calculati on

[Moore, Jonathan (J)]

Here's an update on my effort to reproduce the free energy of solvation difference between cellononaose and 2,3,6-trimethylcellononaose in water at 300 K (the T wasn't specified in the paper but Yu told me that it was 300 K) as reported in the following reference:

H. Yu, M. Amann, T. Hansson, J. Köhler, G. Wich, and W. F. van Gunsteren. "Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study." Carbohydr. Res., 339, 1697-1709 (2004).
	http://dx.doi.org/10.1016/j.carres.2004.05.003

My latest calculation produced a value 444 kJ/mol compared to the reported value of 393.  Given the uncertainty in both values, I'm happy with that level of agreement.  I plan to try a few other cases for confirmation.

Here are the things that I fixed between my first try and the latest:
- use soft cores since the polar hydrogens that are being changed into methyls have no vdw interactions
- specify the A and B state masses explicitly in the [ atoms ] section of the topology file instead of relying on their definition in the [ atomtypes ] section of the ff45a4nb.itp file
- define B state parameters for angles, torsions, etc. that involve perturbed atoms even if that particular interaction doesn't change
- use the -maxwarn option of grompp because of all of the (spurious?) "No default Proper Dih. types for perturbed atoms, using normal values" warnings that it generates

Thanks,
Jonathan

____________________________
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
1702 Building, Office 4E
Midland, MI 48674  USA
Phone:  (989) 636-9765 
Fax: (989) 636-4019
E Mail: jmoore2 at dow.com