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Bug #348

Hanging / Segfaulting Gromacs

Added by schrader empty almost 10 years ago. Updated almost 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Created an attachment (id=391)
two topol.tpr files

I'm using the very latest gromacs version.

Using two quite similar configurations (one without and one with very few water molecules) gromacs ends up in either hanging at step 600 oder segfault after step 400.

Archive.tar.gz (545 KB) Archive.tar.gz two topol.tpr files schrader empty, 09/24/2009 05:27 PM

History

#1 Updated by Berk Hess almost 10 years ago

You system seems to be simply instable.
mdrun -pforce 10000
will tell you that large forces start appearing at some point.

These kind of problems can not be detected easily in an
automated fashion. With constraint you would have probably
gotten constraint warnings before the hang/crash.

Your systems seems very unequilibrated.
Also I don't understand why you are running without constraints
and a timestep of 1 fs, you should probably use 0.5 fs.
But why not use bond constraints?

Berk

#2 Updated by schrader empty almost 10 years ago

I'm beginner, but will try with constraints / different timestep.
Thanks a lot for your answer!

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