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

David spoel at xray.bmc.uu.se
Tue Jan 27 17:31:00 CET 2004

On Tue, 2004-01-27 at 15:44, 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.

have you defined improper dihedrals for the rings? Of course there is
fluctuation in the position, but on average the ring should be flat. If
you get puckering like in cyclohexane your topology is definitely not
OK. same for triple bonds.

> thanks
> dele
> ______________________
> Bamidele Adisa
> Dept of Chemical Engineering
> Clemson University
> Clemson, SC 29634-0909
> 864-654-0586
> ______________________
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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