Toy-MD

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!