HI friends Thanks for your instant help. I got TFE (trifluoroethanol) itp, pdb and gro files. Now I want to disturb you again for a command. I have one TFE molecule. I want to make a solvent box with 100 TFE and 600 Water molecules. What are the commands to translate this one TFE to 100TFE in a mixed solvent box? [I found the water box filled with water in share/tutor/water.] Sorry to bother you, But it seems to be that you guys are my teachers of GROMACS as I am just a 4 days old baby in gromacs. Chiradip
--- David van der Spoel <[EMAIL PROTECTED]> wrote: > Paul van Maaren wrote: > > On Sunday 12 November 2006 10:42, Tsjerk Wassenaar > wrote: > > > >> Probably someone will have a topology and a > structure file for TFE > >> lying around (not me). But TFE isn't the worst of > molecules and since > >> your new with Gromacs, I think it would be an > excellent opportunity to > >> get acquinted with the program and force fields > by parameterizing it > >> yourself. Find the paper of your favorite force > field (choose one) and > >> check how the parameterization of the building > blocks / molecules was > >> done. Take the same steps for TFE. > >> > >> Maybe this isn't the answer you'd hoped for, but > think of the saying > >> "give a man a fish and he can eat for a day; > teach a man how to fish > >> and..." :) > > > > That's always a good approach, but for starters > you might want to take a look > > at tfe.itp in the share/top directory. > > > ... and check recent literature. IIRC there is a > quite recent TFE model > for GROMOS-like force fields. > > -- > David. > ________________________________________________________________________ > 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 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > Send instant messages to your online friends http://uk.messenger.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php