[gmx-users] periodic molecule

CHEN Pan evan.pan.chen at gmail.com
Mon Nov 9 12:55:11 CET 2015

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

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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

Pan Chen
Postdoctoral Associate
Tailor-Made Fuels from Biomass
AICES Graduate School
RWTH Aachen University
+49(0)241 8099205

More information about the gromacs.org_gmx-users mailing list