Here you go.
#$ -S /bin/bash
#$ -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
Director of Research Computing, IT
Adj. Asst. Professor, ECE and Physics
Michigan Technological University
P: (906) 487-4096
F: (906) 487-2787
On Thu, Aug 10, 2017 at 8:38 AM, Subashini K <subashinik2...@gmail.com>
> 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?
> 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
>> 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
>>> #$ -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?
>>> users mailing list
> users mailing list
users mailing list