[gmx-users] periodic molecule

[CHEN Pan]

To set up an infinite cellulose chain, you need:

1): Set up" periodic_molecules = yes" in your mdp file.
2): Built the connection, such as bonds, angles, dihedrals and 1-4 pairs
between the last residue and the first residue in your topology file.
Infinite chain usually means the end of molecules is linked to itself,
which is the mirror of the head groups. You need to process by your own
script.

That's all. Good Luck!

2015-11-09 9:41 GMT+01:00 Pierre-André Cazade <pierre.cazade at ul.ie>:

> Dear GMX users,
>
> I am currently simulating a system involving an infinite slab of
> cellulose. To model it properly, I need each cellulose chain to be a
> periodic molecule. I assume the keyword "periodic-molecule" is there to
> provide such a feature. However, it is not clear from the manual how one
> can build a periodic molecule. Does it require a particular residue
> definition in the ff files or in the topology ones? What are the options
> one must use with pdb2gmx and with grompp?
>
> Thank you in advance for your help.
>
> Best regards,
> Pierre Cazade
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-- 
Pan Chen
Postdoctoral Associate
Tailor-Made Fuels from Biomass
AICES Graduate School
RWTH Aachen University
+49(0)241 8099205