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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