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.caz...@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-requ...@gromacs.org. > -- Pan Chen Postdoctoral Associate Tailor-Made Fuels from Biomass AICES Graduate School RWTH Aachen University +49(0)241 8099205 -- 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-requ...@gromacs.org.
