Simply put the system can't find your gromacs binary that is what the
"gmx: command not found" means.
Just edit your submit script to pass the full path to gmx and you should
be fine
-Chris
Subashini K <mailto:subashinik2...@gmail.com>
August 10, 2017 at 7:59 AM
Hi sun grid engine users,
I am new to scripting.
I want to run GROMACS MD simulations in sun grid engine through qsub
command.
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -N smp1
#$ -l h_vmem=1G
gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq
The above contents were in submit.sh file.
When I gave, qsub submit.sh,
I got the following error
/opt/gridengine/default/spool/compute-0-31/job_scripts/4423509: line
8: gmx: command not found
What am I supposed to do? I intend to do single processor serial job.
How to rectify it?
Thanks,
Subashini.K
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