Hi, If you turn all bonds to constraints, and your system is infinitely periodic, you probably don't even need impropers. The bond lengths can only be satisfied in the plane. Adding impropers, straining your molecule further into the configuration you think is proper, adds forces that inevitable come with vibrations. The higher the straining (the forces), the higher the frequencies, the smaller you have to set your time step to be sure not to get into trouble. Then again, everything moves and surely graphene sheets vibrate. The big question here is: what is the out of plane vibration of atoms in a graphene sheet? Googling "graphene out plane vibration" gives the following for a first hit: http://www.iop.org/EJ/article/0370-1301/69/12/319/prbv69i12p1326.pdf Maybe that's a good start to get your system tuned?
Cheers, Tsjerk On Tue, Aug 11, 2009 at 9:41 PM, Justin A. Lemkul<jalem...@vt.edu> wrote: > > > Darrell Koskinen wrote: >> >> Dear GROMACS Gurus, >> I assigned improper dihedrals to my graphene structuure but still see it >> vibrating. Is this to be expected? I thought the purpose of improper >> dihedrals was to keep planar structures planar. >> > > There is still a force constant associated with the improper, so deviations > from absolute planarity are possible. Vibrations aren't unexpected, but any > severe distortions would be problematic. > > -Justin > >> Here is a copy of a couple of sections of my topology file after assigning >> the improper dihedrals to my graphene structure: >> >> #define improper_dihedral improper_Z_CA_X_Y >> >> [ dihedrals ] >> ; ai aj ak al funct c0 c1 c2 >> c3 c4 c5 >> 3 1 2 5 1 improper_dihedral >> 2 1 3 7 1 improper_dihedral >> 2 1 4 9 1 improper_dihedral >> 1 2 5 11 1 improper_dihedral >> 1 2 6 13 1 improper_dihedral >> >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
