[gmx-users] periodic moleules

Andrei Neamtu neamtuandrei at gmail.com
Tue Sep 1 09:37:11 CEST 2009


I am trying to build a hydrogel polymeric system and I want to make
use of the option periodic_molecules.
In this regard I am a little bit confused..... are there any other
keywords except the option 'peridic molecules' that I have to set to
define a periodic polymer chain e.g. in the molecular topology file?
Because in the case  I define a bond between the last atom of the
chain and the first one, how does the grompp and mdrun know that the
molecule is periodic and not cyclic?

I also suppose that the angle and dihedrals that cross the periodic
border should also be defined.

Is there a place where I can find how to define periodic molecules in Gromacs?

Thanks a lot for any suggestions,


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