by the way also I'd like to know what options for the pbc should I specify that my system looked like infinite lattice in the x-y dims ?
James 2013/1/2, James Starlight <jmsstarli...@gmail.com>: > Bogdan, > > Thank you for explanation. Indeed the problem was in the LINCS > constrains which was not required for the lattice system. > > 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 ? > > James > > 2013/1/2, Bogdan Costescu <bcoste...@gmail.com>: >> On Wed, Jan 2, 2013 at 1:15 PM, James Starlight <jmsstarli...@gmail.com> >> wrote: >>> so why my simulation of the sp3 lattice have been crashed with the >>> links warnings ( which always tells about wrong geometry in topology)? >> >> I might have missed something from the beginning of this discussion... >> Why do you use LINCS with a lattice ? What do you expect to obtain ? >> LINCS is normally used to keep bonds at their equilibrium length. If >> you do this in a lattice, the degrees of freedom will be strongly >> reduced, due to the coupled/restricted motions. How does this >> influence what you want to observe ? If you are not interested in the >> flexibility of the lattice itself, have you considered freezing it ? >> >> 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 >> > -- 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