[gmx-users] Non-planar phenyl rings and non-linear triple bonds

Anton Feenstra feenstra at chem.vu.nl
Wed Jan 28 09:09:02 CET 2004

Bamidele Adisa wrote:

> Hi,
> I'm trying to run an EM (steepest descent) on a pheylacetylene oligomer 
> in a box of water
> using both the OPLS/AA  and GROMACS forcefields.
> what i observed in both situations is that in the output, the phenyl 
> rings turn out to be
> non-planar while the triple bonds turn out to be non-linear.
> could u think of reasons why this is occuring  and probably suggest any 
> solutions to this.
> i used the default parameters for both the OPLS and GROMACS.
> triple bond parameters used for GROMACS forcefield  were obtained from 
> quantum mechanical energy minimizations.

Aromatic rings are kept planar in Gromacs (as well as in OPLS, I presume)
by improper dihedrals, which are basically steep harmonic potentials on
a set of dihedral angles througout the ring system. They still allow some
measure of flexibility. This is what you are observing. It is not necessarily
a problem that needs fixing.

An alternate way of building such a group is using three atoms which have
all the mass of the ring concentrated with contstraints to fix their
relative positions, and construct all other atoms as 'dummy atoms' from
these three. This is described in my thesis (7.	K.A. Feenstra. Doctors
Thesis “Long Term Dynamics of Proteins and Peptides.” Groningen, 2002.
ISBN: 90-6464-992-8. http://www.few.vu.nl/~feenstra/thesis.pdf) as well
as in the Gromacs manual (pdf version). pdb2gmx can convert the normal
'construction' into the 'dummified construction' for the natural aromatic
amino acids (option -dummy aromatics).

Similar ways to construct linear arrangements of atoms (as in a triple
bond), were discussed on the list in the context of molecules like CO2.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

More information about the gromacs.org_gmx-users mailing list