[gmx-users] Implicit solvent models in Gromacs ?

[David van der Spoel]

On Tue, 11 Dec 2001, Marc Baaden wrote:

>I was wondering wether anyone has ever used any type of implicit solvent model
>with Gromacs, however simple or complicated, and what their experiences were.
>
>As far as i could understand from the manual, e.g. a simple model like a distance
>dependent dielectric is not easily possible (not with standard mdp options).
You have to make a user defined potential (using tables).
You can then use V=1/r^2 for the Coulomb if you so wish, but check your
units! People usually have this when r is in Angrstrom, so in the GROMACS
case you need a factor 10 somewhere. Check the file table6-12.xvg in the
top directory, that you have to modify, and then pass it to mdrun.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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