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 .


.. Links

.. _ssh: http://linux.die.net/man/1/ssh
.. _scp: http://linux.die.net/man/1/scp
.. _rsync: http://linux.die.net/man/1/rsync
.. _module system: http://modules.sourceforge.net/
.. _module: http://linux.die.net/man/1/module

.. _OpenPBS: http://www.pbsworks.com/