Here you go.

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


Just a word of caution:

Looking at the path to the Gromacs installation folder, it resides under
"root". In most computing clusters, the /root partition is local to each
compute node. That is, the contents of one node's root folder cannot be
seen by another compute node. A workaround for this problem would be
compile your software in a common folder that is seen and accessible by all
nodes.


Best regards,
Gowtham

--
Gowtham, PhD
Director of Research Computing, IT
Adj. Asst. Professor, ECE and Physics
Michigan Technological University

P: (906) 487-4096
F: (906) 487-2787
https://it.mtu.edu
https://hpc.mtu.edu

On Thu, Aug 10, 2017 at 8:38 AM, Subashini K <subashinik2...@gmail.com>
wrote:

> Thank you for the reply.
>
> How do we do it?
>
> It is located in /root/usr/local/gromacs/bin/gmx
>
> What would the correct command then?
>
> Can you please let me know?
>
> Thanks,
> Subashini.K
>
>
>
> On Thu, Aug 10, 2017 at 5:45 PM, Chris Dagdigian <d...@sonsorol.org> wrote:
>
>>
>> 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
>>> _______________________________________________
>>> users mailing list
>>> users@gridengine.org
>>> https://gridengine.org/mailman/listinfo/users
>>>
>>
>>
>
> _______________________________________________
> users mailing list
> users@gridengine.org
> https://gridengine.org/mailman/listinfo/users
>
>
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