Yes. I did this way. I wrote it in small awk script. If you like I can share with it.
Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Friday, April 06, 2007 4:11 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] modify C6 directly in FF using sigma and epsilon David Mobley wrote: > David, > > I'm using 3.3/3.3.1. > > Is there an easy tweak to the source code that would allow something > like this? i.e. could I somehow easily tweak the bit where it reads > the nonbond_params section so I can use an alternate combination rule > there by specifying, say, a different nonbonded parameter type? > It doesn't look like it. The sigma and epsilon are first read in the atomtypes section, and a matrix is filled in with sigma and epsilon. Then, if you overwrite a pair in the nonbond_types section two (because f symmetry) matrix elements are replaced. Finally, just before writing the file the values are converted to C6 and C12. It seems that your best bet is to write that little Perl script to convert the whole force field to C6/C12. -- 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 search the archive at http://www.gromacs.org/search before posting! 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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