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

David Mobley dmobley at gmail.com
Thu Jan 26 16:15:48 CET 2006


That sounds better. Have you done any error analysis? (i.e. with
calculating correlation times). Also, it is worth looking to see
whether the Yu paper used soft cores? In my experience there is still
a lot of published work which doesn't use soft cores, and this makes
me skeptical whether it can be trusted.

I don't know if you plan to publish this particular work, but it is
always useful, IMO, to have these sorts of calculations as a
benchmark: As you've found out, it can be nontrivial to reproduce
published work (and indeed, sometimes it isn't reproducible); anytime
there *is* reasonable agreement, it's worth getting it out there so
people can use it as a test case to make sure they're doing things


On 1/26/06, Moore, Jonathan (J) <JMoore2 at dow.com> wrote:
> 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
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