[gmx-users] program crashed

Dongsheng Zhang dong at pampas.chem.purdue.edu
Wed Jul 5 08:14:15 CEST 2006


I have written a new force field for my polymer. I have used this force
field for polymer in water. It worked fine. When I tried to put polymer
with nanotube in water, then I had this strange problem (My force field
worked fine for nanotube alone). Anyway I will try to rerun it.

Thank you for your help!


On Wed, 2006-07-05 at 16:04 +1000, Mark Abraham wrote:
> > On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote:
> >> > Mark,
> >> >
> >> > 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).
> >>
> >> OK... bonds don't just "break" in MD simulations. Bonded potentials
> >> don't
> >> allow for it, and often bond-length constraint algorithms are being used
> >> anyway.
> >  That is what I expect. However I find some atoms are far away from
> > others from step38885.pdb even though I have used all-bonds constraint.
> > Do you have any idea what's going on? Thank you for your help!
> I don't have many further ideas. You have a bunch of atoms that appear to
> have moved around messily. If your visual check of the trajectory is valid
> then there shouldn't be anything wrong with your topology, but it might be
> worth checking. Maybe try re-running the calculation keeping lots of
> velocities and positions so you can do restarts close to the problem area
> and get more info...
> Mark
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