rainy...@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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