HOW TO RUN THE MOLECULAR DYNAMICS EXERCISES

(1) Launch python or ipython.
    (a) Running from Cornell in the physics facilities in the 
    basement of Rockefeller, just log in.
    (b) Running remotely from another machine with X-windows, if you have
    an account on one of the Rockefeller machines,
	ssh -X username@remote.physics.cornell.edu
	ssh -X wsNN	[login to one of the client machines, where NN is
       			an integer from zero to around 30. The server doesn't 
			have user software installed.]
    (c) If you aren't from Cornell physics, log on to a machine with Python
    and the necessary packages installed. Installation instructions for Linux,
    Windows, and Macs at http://www.physics.cornell.edu/~myers/teaching/ComputationalMethods/python/WorldPy.html

(2) Copy DigitalMaterial.py and PairDistributionMD.py (or the python answer
file for your exercise) from the Web site into the current directory

(3) Run the demo, to get a quick run-through of the whole sequence of
simulations. Note: indents must be consistent in Python; no spaces
before these lines...

    ipython
    In [1]: %run PairDistributionMD	# or the corresponding exercise.py file
    In [2]: demo()

--- or, if you don't have ipython installed ---

    python -i PairDistributionMD.py    

You will need to say "y" to continue between steps. You may need to kill
the plot to restart the simulation as well.

(4) Run
    In [55]: demo(nAverages=10, nCoolSteps=4)
or something similar, to get better thermalization (nCoolSteps) and 
better statistics for the histograms (nAverages).

You can get plots of the histograms by clicking on the save-disk 
at the bottom. The red curve for the gas simulation is the theory curve.