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

Moore, Jonathan (J) JMoore2 at dow.com
Thu Jan 26 14:51:51 CET 2006

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).

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


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

More information about the gromacs.org_gmx-users mailing list