Example run

Let’s run our Argon simulation on saguaro. You need to prepare the binary run input file (the “TPR file”) md.tpr as described in the last practical. It contains all information for Gromacs to run the simulation. Right now you can use one I prepared.

Let’s practice the work flow:

Get the file on your local computer (iMac, workstation):

curl -O http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/12/Argon_input_files.tar.bz2
tar -jxvf Argon_input_files.tar.bz2
cd Argon_input_files

Copy the TPR file to saguaro:

scp md.tpr ASURITE@saguaro.fulton.asu.edu:P12

Log in to saguaro (ssh) and now on saguaro, set up the queuing system script.

cd P12
curl -O http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/12/saguaro_gromacs.pbs

• change the jobname to “Argon”
• change the run time to 5 minutes
• change the number of nodes to 2

Run the job:

qsub saguaro_gromacs.pbs

Check status:

qstat

and also look at the output files such as md.5805254.newmoab.local.out.

When done, copy everything back to your workstation (e.g. use a different terminal or log out from saguaro):

scp -r ASURITE@saguaro.fulton.asu.edu:P12 .