[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.
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users