[gmx-users] program crashed

Mark Abraham mark.abraham at anu.edu.au
Wed Jul 5 08:04:23 CEST 2006

> 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...


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