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

Bamidele Adisa badisa at CLEMSON.EDU
Tue Jan 27 15:59:00 CET 2004

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.

Bamidele Adisa
Dept of Chemical Engineering
Clemson University
Clemson, SC 29634-0909

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