At parties, people often ask me what I do. Normally I answer that I simulate molecules on a computer. Most people seem satisfied with that answer, after all, it’s only an ice-breaking question (people are secretly hoping for something like “sex-worker” or “published novelist”). But if I actually get someone who wants to know, then I’ll give an impromptu explanation, complete with flying arms and sound effects.

But really, the best way to understand what I do is to watch a movie, a movie of a simulation that is. Probably the simplest type of protein simulation you can do, is to simulate the neuro-peptide met-enkephalin. It is the default molecule that simulators use when they want to test a small peptide. Here is a movie of met-enkephalin in a box of water molecules:

This is an example of a molecular dynamics simulation. Molecular dynamics use Newtown’s equations to integrate the equations of motion, and pretends that quantum mechanics doesn’t really exist and that chemical bonds can never ever break. The grey molecule in the middle is the met-enkephalin, a tiny peptide that is released by the brain and modulates part of the pain when say, you shoot a nail into your forearm. The read balls are the water molecules. The movie shows a cross-section of the simulation.

Met-enkephalin is a peptide (or a very very small protein) in that it is made up of 6 amino acids H2N-Tyr-Gly-Gly-Phe-Met.

In the simulation, we simulate met-enkephalin in a bath of water because inside the cell, there’s lots of water. The standard way of simulation water is to put in a box, and then to slap on a periodic boundary condition. 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 are gaps near the molecule. You will see these gaps fill up.

What dictates the time-scale of this simulation (overall about 100ps or 0.0000001 s)? Well, it turns out that the integration step of molecular dynamics depends on the smallest kinds of motions allowed using this level of approximation. It depends on a bond vibration. Typically, the step size for the integrating step of the equations is 1 fs (0.000000000001s), or about 1/10th the time it takes for a bond to vibrate.