[gmx-users] Implicit solvent models in Gromacs ?
David van der Spoel
spoel at xray.bmc.uu.se
Wed Dec 12 09:31:36 CET 2001
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.
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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