Molecular dynamics simulations

I use molecular dynamics simulations to study huge molecules like proteins, the molecular machinery cells use to accomplish almost all functions which sustain life. These simulations give us a way to 'watch the movie' of how these molecular "machines" perform their functions. The work by an interative process:

Step 1: Calculate the forces acting on each atom by every other atom.
Step 2: Calculate how the forces will move the atoms by integration of acceleration into velocity.
Step 3: Move all the atoms, and go back to Step 1.

Interestingly, a similar algorithm to MD is used to study the motions of stars and galaxies, since both molecular (charge-charge or electrostatic) and galactic motion (large bodies of mass attracting each other via gravity) are dominated by inverse-square-distance laws, respectively: $$ \displaylines{ F_{gravity} = k_g \frac{m_1 m_2}{r^2} \\\ F_{charge} = k_e \frac{q_1 q_2}{r^2} } $$ This means that a lot of the world's supercomputer time is spent similar calculations whether astrophysical or biophysical. It is still an evocative mystery why there is this symmetry between the forces acting on stars and on atoms.

If you want to get an idea about how MD works, you can play with this free, online interactive MD simulator, or you can fall down the MD Wikipedia rabbit hole.