Hi there,
I have been using GROMACS version 5.0.6 to perform some simple MD
Simulations that involve a polystyrene strand and a single further
molecule (e.g. toluene). I wanted to observe some angles between both
molecules so after I produced a trajectory, I applied "gmx gangle" and
everything worked just perfectly. I subsequently employed a topology in
which I did not change anything except that I assigned zero-charges
(instead of standard OPLS-AA values) to all atoms and produced another
trajectory.
In this case analysis with "gmx gangle" immediately aborts with:
.../gromacs-5.0.6/src/gromacs/gmxlib/pbc.c, line: 81
Fatal error:
Unknown ePBC=38063816 in ePBC2npbcdim
I am following basic procedures with these simulations, since I have not
much experience in MD. However, I think this is a bit odd and probably
not my fault? I further guess that, since I have trajectories, I can
also utilize something like vmd or travis to also get the angles I am
interested in?
Thank you and best regards,
Thomas Niklas
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