[gmx-users] Segmentation fault while running MD simulation

[Amit Choubey]

hi,

could you specify the system size?

How many steps did it run before you got the segmentation fault? Try to find
if everything went ok until the segmentation fault by saving log and
trajectories.

amit



On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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