[gmx-users] periodic moleules

Berk Hess gmx3 at hotmail.com
Tue Sep 1 10:02:30 CEST 2009


If something is periodic or cyclic only depends on the coordinates,
in the topology there is no difference.
That is the reason for the periodic_molecules mdp option.

You will have to manually add the bond, angles, dihedrals and pairs
for the periodic (or cyclic) bond to the topology.


> Date: Tue, 1 Sep 2009 10:37:11 +0300
> From: neamtuandrei at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] periodic moleules
> Hi,
> 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,
> Andrei
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