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


Subashini K <>
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.

#$ -S /bin/bash
#$ -cwd
#$ -N smp1
#$ -l h_vmem=1G
gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq

The above contents were in file.

When I gave, qsub,

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?

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