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 _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
