This is a tiny repository with Python code to play with molecular dynamics (MD) simulations. It can be extended for testing and trying new algorithms or potentials.
Disclaimer: the stuff in here is not suitable for production simulations.
Example for running: % ./toy_md.py -h
This will give you the command line help for the script.
% cd carbon-dioxide
% ../toy_md.py -c co2.pdb -p params.txt -f force_field.txt -w co2-output.pdb
And similar in the other directories.
Then open the resulting traj.pdb with a viewer of your choosing, but you can use the simple PyMoL script for the purpose.
Enjoy Toy-MD!
There are a few small scripts for educational purposes here as well.
- maxwell.py will generate a Maxwell-Boltzmann velocity distribution and plot it
- zwanzig.py will generate energy data sets and compute the Free energy according to the Zwanzig formula