[gmx-users] Non-biomolecular systems on Gromacs: incorporating a force field

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 16 21:44:42 CEST 2006

Marin Djendjinovic wrote:
> Hi All,
> I have couple of newbie questions that I hope someone will have
> patience to answer.  I have some experience with MD
> simulation and none with Gromacs.
> I have been using Tinker package for about half a year, but I
> find it a little unfriendly (not a very thorough manual and it's
> written in Fortran which is not my cup of tea :)) 
> I see that most of tutorials and explanations on Gromacs site are
> related to proteins. Is there a reason Gromacs would not be a
> good choice for other systems, such as silica, for example?
> I would like to incorporate force field for silica in the
> Gromacs. Now where do I start? What source files would I need to
> modify? It's OK if you can't give me a detailed answer, but at least
> a starting point, a little bit more then that flow chart on the
> Gromacs website.

If you have starting coordinates, please try the x2top program. It works 
best in the CVS version which is a bit more tricky to compile.

> Thanks for your help.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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