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.
_______________________________________________
gmx-users mailing list [email protected]
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
--
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
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
