Dear David I have taken a look to the manual (version 3.3) and I haven't found information about how to tabulate bonded potential functions (it seems that Ran is right). On the other hand, what do you mean exactly with adding two dihedrals?
Angel Pineiro. > Date: Tue, 29 Jan 2008 19:18:20 +0100 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] torsion potential with 7 parameters > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > ngel Pieiro wrote: > > Hi all, > > anyone knows how to use (in gromacs) a potential of the type: > > > > U_tors(phi_ijkl) = Sum_n 1/2 k_n [1-cos(n phi_ijkl)] > > > > with n going from 1 to 7? > > > > as far as I saw only the Ryckaert-Bellemans with 6 parameters and a > > periodic function are implemented in gromacs. Chapter 4 says something > > about this subject and it explains how to translate OPLS in R-B but it > > seems that 7 parameters are not included > > > > I am trying to use the force field for perfluoroalkanes published by > > Borodin et al in JPCB (106) 2002, 9912. > > > in the worst case you can add two dihedrals, however n = 6,7 is not > implemented. you can however tabulate this if I'm not mistaken. > > > Thanks in advance for the help, > > > > Angel Pieiro. > > > > _______________________________________________ > > 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > ------------------------------ > > Message: 4 > Date: Tue, 29 Jan 2008 19:26:06 +0100 > From: Ran Friedman <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] torsion potential with 7 parameters > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8 > > David van der Spoel wrote: > > > > in the worst case you can add two dihedrals, however n = 6,7 is not > > implemented. you can however tabulate this if I'm not mistaken. > Isn't the bonded tabulated paramers due only in GMX 4.0? > Ran. _______________________________________________ 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
