1__2 6__ // 3\/ \\ | ||4 | \\___ /\___// 5 7
I want to know if 1-2-3-6 torsion should be included? And if both 2-3-4-7 and 6-3-4-5 should be included? Thanks. Ming On Tue, Apr 27, 2010 at 6:43 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Ming Han wrote: >> >> Dear all, >> >> I want to test a MD simulation job for the naphthalene molecule by the >> oplsaa force field by. The x2top generated less number of dihedral >> angles than what I expected. Do you know how many dihedral angles >> should be included for the naphthalene molecule if I use oplsaa? > > It would be helpful to see the [dihedrals] directive that x2top produced, as > well as an explanation of what you think you should've gotten. Just saying > you got less than what you thought isn't very informative. You may also > want to consult the primary literature for OPLS to see the derivation of > bonded parameters and how they might be applied to naphthalene. > > -Justin > >> >> Thanks a lot. >> >> Ming > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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-us...@gromacs.org > http://lists.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 > -- gmx-users mailing list gmx-users@gromacs.org http://lists.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