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
>>
>
>
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