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
