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 <[email protected]> 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:[email protected]> >> 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 >> [email protected] >> https://gridengine.org/mailman/listinfo/users >> > >
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