[gmx-users] program crashed

Dongsheng Zhang dong at pampas.chem.purdue.edu
Wed Jul 5 06:18:35 CEST 2006


Thank you for your reply. When I checked step38885.pdb, I found a
polymer chain in my system fall apart (bond broken). If I visualize the
trajectory. it is fine till step38000 (last frame in my trr file).

I don't understand why the bond breaks after 76 ps simulation and why KE
doubles suddenly. Do you have any idea what's wrong?

All the best!


On Wed, 2006-07-05 at 13:54 +1000, Mark Abraham wrote:
> > Dear GMX users,
> >
> > After I edit vdwradii.dat and run genbox, my program still crashes when
> > I run position restrained MD with heating the system from 100K to 300K.
> > When I check the log file. I find the kinetic energy doubles (step 38880
> > compare to step 38870, by the way, the re_t is the same in these two
> > steps) when the constraint problem starts to take place. Does anyone
> > know why KE doubles?
> Have you visualized the trajectory to see where things start going wrong?
> Mark
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