At parties, when people ask me what I, I tell them I simulate protein molecules. So what do I mean by that?
Simulating a very small peptide in water
Probably the simplest type of protein simulation you can do, is to simulate met-enkephalin. This is because:
it is a peptide, or a very small protein; it is made up of amino acids, which most simulation packages handle
it is small - only 6 amino acids, it's chemical name is H2N-Tyr-Gly-Gly-Phe-Met; the typical protein is ~300 amino acids
it is important - these babies are neuro peptides; they are released by the brain to stimulate opiod receptors in the rest of your body, say, when you accidentally shoot a nail into your forearm.
It is now de riguer to simulate peptides in a box of water molecules because inside the biological cell, there's lots of water. And during th simulation, periodic boundary condition apply: a water at the edge of the box will feel the effects of a water from the other side of the box. Otherwise the water molecules will just float off into space.
In the beginning of the simulation, the water molecules are arranged in some kind of auto-generated starting position. There will be gaps near the molecule. You will see these gaps fill up.
This following is a movie of a molecular dynamics simulation of met-enkephalin.