A schematic showing how a molecular dynamics simulation is performed. First, a computer model of the receptor-ligand system is prepared. An equation like that shown in Figure 3 is used to estimate the forces acting on each of the system atoms. The positions of the atoms are moved according to Newton's laws of motion. The simulation time is advanced, and the process is repeated many times. This figure was adapted from a version originally created by Kai Nordlund.
Durrant and McCammon BMC Biology 2011 9:71 doi:10.1186/1741-7007-9-71