On Wed, Jan 2, 2013 at 2:58 PM, James Starlight <jmsstarli...@gmail.com> wrote: > By the way now I'd like to simulate the same 2D flexible ( in non > planar hybridization) lattice but consist of non-hydrogens atoms only > ( only atoms forming lattice scaffold ). Does it possible to change > Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry > ( >c- ) or should I use anothe atom type for such lattice ?
I can't imagine how it can be both "non planar hybridization" and "preventing tetragonal-like geometry", but maybe I don't understand your intentions. Assuming you do want a change in geometry - from tetragonal to planar - then you need to use different parameters to describe the different geometry, it's not only about changing valence. If you use OPLS-AA, this means a change of atom type from something like C sp3 (f.e. opls_139) to sp2 (f.e. opls_147) - both these types chosen for having zero charge. Cheers, Bogdan -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
