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| Name | Last modified | Size | Description |
|---|---|---|---|---|
| Parent Directory | - | ||
| hoscmd_v0.py | 2013-02-14 15:46 | 5.4K | |
| VerletIntegrator3D/ | 2013-02-14 11:34 | - | |
| Practical07Verletintegratorin3D.pdf | 2013-02-14 11:34 | 58K | |
| p07_class.txt | 2013-02-14 11:34 | 1.9K | |
| mdIO.py | 2013-02-14 11:09 | 5.3K | |
| hosc_ao.mov | 2013-02-13 22:55 | 170K | |
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 hoscmd_v0.py as basis.
mdIO.py 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.