Hi all, I am hoping someone could give me advice regarding a topology file design.
I am trying to implement a forcefield for an organic crystal with 30 atoms at each site (therefore, 30 atom basis). Sites are connected by an aromatic ring. The forcefield I am trying to implement does not treat ring as a single unit; rather, carbons are a part of the 3- and 4- body interactions with other atoms from the site, and two of them have harmonic term between themselves. Initially, I tried to set each (30-atom) site as one "moleculetype". So, half of the aromatic ring would be in one "moleculetype", and half of it in the neighbor. But then I have to set up BONDED interactions between atoms from DIFFERENT molecules. And not just one, three of them: torsion, angle term and multiple harmonic terms. I was hoping someone could see a solution here. I tried regrouping ring carbons to different molecules (sacrifising symmetry) but I always end up with a bonded interaction between "nonbonded" atoms. Any suggestion is appreciated. F. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
