[MMTK] Trying to understand the example

[Konrad Hinsen]

> With Konrad's help, I succeeded to run the example in the manual, page
> 15. Now I am trying to understand what is happening physically. The
> example contains

This is of course not a realistic and useful simulation, just a script that 
illustrates some important aspect and runs very quickly.

> So what is happening here? If I understand correctly, I created a single
> water molecule. Why is universe.molecule set up so that it refers to one
> molecule only?

The only answer is "why not?"  Assigning a molecule to an attribute of a 
universe is one way of putting it in there. You could also do it anonymously 
by

  universe.addObject(Molecule('water'))

> Then, when we are integrating the trajectory, why would this single
> molecule move at all, except due its initial velocity? In other words,
> which force can be acting on this molecule if there is only one molecule

There is no global force on the molecule, so it moves only because of its 
initial velocity. There are however internal forces that keep the vibrations 
going.

>   in the universe? Where does the potential energy come from? Or is

Bond and angle terms. You can find it out printing

  universe.energyTerms()

> I guess that I am missing something basic here.

No, you are just looking for too much physics in the example. However, just 
replace Molecule('water')  by Protein('insulin'), and the same script will 
suddenly look much more useful. Or take a look at the example directory, 
there are more useful scripts there as well.

Konrad.
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