[gmx-users] periodic molecule

Pierre-André Cazade pierre.cazade at ul.ie
Mon Nov 9 14:11:14 CET 2015

Thanks a lot.


On 09/11/15 11:54, CHEN Pan wrote:
> 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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