[gmx-users] Designing a topology file: bonded/non-bonded mess

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 14 12:12:55 CEST 2007

Frankie Montenegro wrote:
> 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.

question: are there chemical bonds between "molecules" (which you seem 
to imply by stating the sites are connected by an aromatic ring). If 
there are then your whole system should be considered as a single 
molecule. Have you tried x2top on this? (gmx 3.3.2 only).

> Any suggestion is appreciated.
> F.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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