Hi,Justin: Thanks for your response.
I have read that part and still confused. Does it mean that if I choose the ffoplsaa.itp in my top, I used the RB potential for Dihedrals or the periodic type? Also actually I can only get the parameters for phi, cp and mult (listed above) Can I use these parameters directly for my itp user ffoplsaa force field? Thanks a lot! 2009/1/28 Justin A. Lemkul <jalem...@vt.edu>: > > > Yanmei Song wrote: >> >> Hi, >> >> I am using ffoplsaa.itp as my force field to do a simulation using >> GROMACS. >> I have a question about how to write the parameters in dihedrals in >> the itp file. >> >> [ dihedrals ] >> ; ai aj ak al fu c0, c1, m, ... >> 1 2 5 6 1 0.0 3.77 3 0.0 3.77 3 ; dih CAA >> CBF OAW CBH >> 2 5 6 9 1 0.0 3.77 3 0.0 3.77 3 ; dih CBF >> OAW CBH OAY >> 5 6 9 10 1 0.0 3.77 3 0.0 3.77 3 ; dih OAW >> CBH OAY CBJ >> 6 9 10 13 1 0.0 3.77 3 0.0 3.77 3 ; dih CBH >> OAY CBJ OBA >> 9 10 13 14 1 0.0 3.77 3 0.0 3.77 3 ; dih OAY >> CBJ OBA CBL >> >> Then if I am choosing ffoplsaa.itp force field, what is the meaning >> for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and >> OPLS force field have a different format for proper dihedrals. For >> OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my >> question is how can i define the dihedral parameters in itp file based >> on ffoplsaa force field in GROMACS? Thanks a lot! >> > > Refer to the manual, section 4.2.12 "Proper Dihedrals." > > -Justin > >> Yanmei > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php