Hi,
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.
Berk
> Date: Tue, 1 Sep 2009 10:37:11 +0300
> From: [email protected]
> To: [email protected]
> 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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