Molecular dynamics simulation
A molecular dynamics simulation of a system is straightforward to perform once a system has been set up and equilibrated.
Several different dynamics algorithms are available but Langevin dynamics is employed in the example program. Each of the four systems is simulated for 100 ps and snapshots are saved at 250 fs intervals giving 400 structures per system for later analysis. Trajectories in Amber format are used as these can be read and visualized by other programs.