[gmx-users] Segmentation fault while running MD simulation

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 14 00:53:28 CET 2009

rainy908 at yahoo.com wrote:
> Hi,
> The relevant lines of my script are the following:
> line 27: # Run MD and write output to /nas2 disk
> line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c 
> confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
> line 29:
> line 30: # MDRUN completes: now make the next run file for a further 200 
> ps, to be run by next job
> line 31: $TPBCONV -s npg3_4.tpr -f npg3_4.trr -e npg3_4.edr -o 
> npg3_4_2.tpr -extend 200000
> Since line 31 would be carried out after line 28, I'm not sure why the 
> comment "-s: command not found" is relevant?

Because mdrun is exiting, so the script is moving on.  Perhaps the system isn't 
recognizing the $TPBCONV environment variable, and thus is interpreting "-s" as 
a separately command rather than an option passed to tpbconv.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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