[gridengine users] RUNNING GROMACS SIMULATIONS THROUGH SCRIPT FILE

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

Re: [gridengine users] RUNNING GROMACS SIMULATIONS THROUGH SCRIPT FILE

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 August 10, 2017 at 7:59 AM Hi sun grid engine

Re: [gridengine users] RUNNING GROMACS SIMULATIONS THROUGH SCRIPT FILE

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 wrote: > > Simply put the system can't find

Re: [gridengine users] RUNNING GROMACS SIMULATIONS THROUGH SCRIPT FILE

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