.. -*- encoding: utf-8 -*-

=========================================
 MD simulation in the canonical ensemble
=========================================

We will be trying the Nosé-Hoover thermostat (see the Gromacs 4.5
manual on pp28, Chapter 3.4.8).

Instead of setting :math:`Q`, we'll specify the period of the
oscillations :math:`\tau_T`

.. math::

  \tau_T = 2\pi\sqrt{\frac{Q}{T_0}}

for a desired temperature :math:`T_0` (this is the definition of
:math:`Q` used in Gromacs). 

We want to see how the oscillaton time influences the thermostat
behavior. Start with :math:`\tau_T = 1 \mathrm{ps}` and then try 0.01
ps and 100 ps.

.. Berendsen: tau = 0.1 ... 0.5 ps
.. N-H: 5x tau_Berendsen


Thermostat selection
====================

Create an appropriate run parameter (MDP file) based on the NVE input
file ``NVE_opls.mdp`` (which does *not* have temperature coupling). 

In particular, pay attention to

- run length (``nsteps``)
- temperature coupling algorithm (see the `Temperature coupling`_
  section in the MDP manual page) --- you need to set coupling time,
  reference temperature :math:`T_0`, and couple the thermostat to the
  whole system (group "SYSTEM")
- temperature: run at 310 K

Use the manual on the `MDP options`_ to write your MDP file. 

.. _Temperature coupling: http://manual.gromacs.org/online/mdp_opt.html#tc
.. _MDP options: http://manual.gromacs.org/online/mdp_opt.html


Make a separate directory for each run that you plan to do. Copy the
MDP file to each directory and adjust it there. You can take the ``water.top``
and ``em.gro`` that you generated previously.

Generate TPR file with grompp::

   grompp -f MDP -p ../top/water.top -c ../emin/em.gro -o md.tpr

Run the simulation::

   mdrun -v -s md.tpr -deffnm md

If it takes too long on your workstation, run it on saguaro on 4 or
perhaps 8 cores.



Running on Saguaro
==================

http://a2c2.asu.edu/rails/topics/first-things-first

- login to saguaro
  (http://a2c2.asu.edu/rails/topics/first-things-first/how_tos/connect-to-saguaro)::

    ssh -l USERNAME saguaro.fulton.asu.edu

- create a work directory for this session (note: you're not sharing
  space with anyone else), eg ::

    mkdir P14

- Transfer TPR file and queuing system script saguaro.pbs::

    scp md.tpr saguaro_gromacs.pbs USERNAME@saguaro.fulton.asu.edu:P14/

- increase wall time from 01:00 minutes to 5:00 minutes; Gromacs will
  stop cleanly after (``-maxh``) 0.0833 * 1h = 5 mins.

  Note: adjust ``-maxh`` depending on your walltime!!

- the ``-A`` switch is important so that the time is billed to the course
  project!


- Submit job to the PBS queing system::

    qsub saguaro.pbs

- Check status::

    qstat

- When done, copy stuff back using ``scp`` or ``rsync``::

    rsync -avP USERNAME@saguaro.fulton.asu.edu:P14/ .

  will copy all contents of director ``P14`` on saguaro to the current
  directory (see man rsync for details).