[MMTK] Trying to understand the example

[Michiel Jan Laurens de Hoon]

Dear MMTKers,

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
.....
 >>> universe = InfiniteUniverse(Amber94ForceField())
 >>> universe.molecule = Molecule('water')
 >>> universe.initializeVelocitiesToTemperature(300*Units.K)
 >>> integrator = VelocityVerletIntegrator(universe)
 >>> trajectory = Trajectory(universe,"water.nc","w")
 >>> integrator(delta_t=1.*Units.fs,steps=50,
                actions=[StandardLogOutput(5),
                         TrajectoryOutput(trajectory,("time","energy",
                                                      "thermodynamic",
                                                      "configuration"),
                                          0, None, 1)])

The output that I get is printed below.
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?

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 
  in the universe? Where does the potential energy come from? Or is 
there an implicit background substance in which the molecule is moving?
I guess that I am missing something basic here.

Thanks in advance,

Michiel, U Tokyo.




Step 0
Time: 0.000000
Potential energy: 0.000209, Kinetic energy: 7.771315

Step 5
Time: 0.005000
Potential energy: 0.110330, Kinetic energy: 7.679841

Step 10
Time: 0.010000
Potential energy: 0.307198, Kinetic energy: 7.525711

Step 15
Time: 0.015000
Potential energy: 0.563593, Kinetic energy: 7.322000

Step 20
Time: 0.020000
Potential energy: 0.642356, Kinetic energy: 7.281926

Step 25
Time: 0.025000
Potential energy: 0.684268, Kinetic energy: 7.264391

Step 30
Time: 0.030000
Potential energy: 0.595910, Kinetic energy: 7.358397

Step 35
Time: 0.035000
Potential energy: 0.591070, Kinetic energy: 7.364905

Step 40
Time: 0.040000
Potential energy: 0.618558, Kinetic energy: 7.330760

Step 45
Time: 0.045000
Potential energy: 0.647354, Kinetic energy: 7.290174

Step 50
Time: 0.050000
Potential energy: 0.637005, Kinetic energy: 7.269806

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon