Molecular dynamics

Molecular dynamics is a way of simulating atoms and molecules on a computer. It steps Newton’s equations forward with empirical force fields, usually in femtosecond timesteps. It’s the workhorse of computational chemistry.

The Atom rung uses the standard all-atom figure of about a thousand operations per atom per femtosecond step.

The Atom rung uses the operations per atom per femtosecond that chemists really use when they simulate a protein. The difference is scale. They simulate millions of atoms for microseconds. The sandbox asks for a whole planet over a century.