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

=======================================
 Practical 07: Verlet Integrator in 3D
=======================================

Harmonic bonds
==============

Your task is to simulate a carbon-carbon bond. 

We model it as a simple harmonic oscillator with masses 6u and force
constant 1860e2 kJ/mol/nm^2 with a reference bond length of 0.15
nm. We integrate the equations of motion with the Verlet algorithm.

* We will treat the two particles as points in 3-space. 
* Outline of code is provided as ``hoscmd_v0.py``.

Task
====

1. Discuss the problem with your neighbors in your row. Derive the
   equations for the potential energy and the force (see Assignment
   04). Note that this should be treated as a 3D problem: input and
   output are points with three cartesian coordinates.

2. Download ``hoscmd_v0.py`` and ``mdIO.py`` from
   http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/07/
   
   Rename ``hoscmd_v0.py`` to ``hoscmd.py`` and work on this code. The
   file ``mdIO.py`` contains updated functions for trajectory output
   (namely :func:`mdIO.write_xyz_frame`).

3. Make the code work. See the comments in the file.

   You may work with your neighbors.

4. Produce a graph of the potential energy over 1000 steps at a time
   step of 0.001 ps (1 fs), initial atom separation of 0.2 nm, and
   initial velocities 0.

5. Visualize the resulting trajectory ``hosc.xyz`` in VMD_ :

   1. Open /Applications/VMD
   2. Menu: File -> New Molecule: browse to ``hosc.xyz`` and Load
   3. Menu: Graphics -> Representations:

      - Drawing Method: CPK

   4. Play trajectory: Main window lower right corner '>'
   5. Rotate with mouse

   You can try to make a movie with Extensions -> Visualization ->
   Movie Maker:

   - Movie Settings: Trajectory
   - Format: try different ones, maybe one works
      
.. _VMD: http://www.ks.uiuc.edu/Research/vmd/

6. As a bonus: also calculate the kinetic and total energy of the
   system and plot.