ProtoMol: A Molecular Dynamics Framework with Incremental Parallelization.
Thierry Matthey, Jesús A. Izaguirre · 2001
Molecular dynamics (MD) for a classical unconstrained simulation of bimolecular systems requires the solution of Newton’s equations of motion. At each step, one evaluates the contribution of interacting forces, and these are applied to the system using a numerical integrator. The most computationally expensive part is the force evaluation among atoms.