Practical Session 07

Files for practical on 2/14/2013. These files will be available for the duration of the course.
[ICO]NameLast modifiedSizeDescription

[PARENTDIR]Parent Directory  -  
[VID]hosc_ao.mov2013-02-13 22:55 170K 
[TXT]mdIO.py2013-02-14 11:09 5.3K 
[TXT]p07_class.txt2013-02-14 11:34 1.9K 
[   ]Practical07Verletintegratorin3D.pdf2013-02-14 11:34 58K 
[DIR]VerletIntegrator3D/2013-02-14 11:34 -  
[TXT]hoscmd_v0.py2013-02-14 15:46 5.4K 

Verlet integrator in 3D

In order to learn how to deal with 3D coordinates in the context of a MD program we study a very simple system: Two C atoms connected by a bond. The bond is modelled as a harmonic force. In Assignment 04 you derived the analytical form of a harmonic force between two particles. You can use this to code the force routine that is used to integrate the equations of motion of the two body system. Use as basis. contains updated functions for writing XYZ trajectories, which can then be viewed.


VMD is a versatile molecular visualization program. It is very good at displaying MD trajectories and is geared towards biopolymers and liquids but it can be used for a wide range of systems.

On the Macs, you will find it in /Applications.