[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 users,

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 your gromacs binary

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 partit

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

Hi, (1) GROMACS is installed in /usr/local/gromacs/bin/ Not in root as I mentioned earlier. (2) When I gave #!/bin/bash #$ -S /bin/bash #$ -cwd #$ -N smp1 #$ -l h_vmem=1G usr/local/gromacs/bin/gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq I got the same error again. But, when I run it directly my

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

Hi, you had a typo in your script (the leading slash in the path), you want: #!/bin/bash #$ -S /bin/bash #$ -cwd #$ -N smp1 #$ -l h_vmem=1G /usr/local/gromacs/bin/gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq for these things it might be more convenient to ask a colleague who has a little experie

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

Is the folder, /usr/local/gromacs, shared across all nodes in your cluster? On Fri, Aug 11, 2017 at 1:59 AM Subashini K wrote: > Hi, > > (1) GROMACS is installed in /usr/local/gromacs/bin/ > > Not in root as I mentioned earlier. > > (2) When I gave > > > #!/bin/bash > #$ -S /bin/bash > #$ -cwd

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

Hi, Can anyone cross check it? If so, how? Or, should we ask the system administrator? Thanks, Subashini.K On Fri, Aug 11, 2017 at 4:37 PM, Gowtham wrote: > > Is the folder, /usr/local/gromacs, shared across all nodes in your cluster? > > > On Fri, Aug 11, 2017 at 1:59 AM Subashini K > wrot

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

ssh into a node and try "which gmx" Either it will be found in your path, or it won't. Or "ls /usr/local/gromacs/bin/gmx" and see if exists. Best to include the full path to the things you need every time. Using "which" makes things a little easier i.e. GMX=`which gmx` and then use $GMX in yo