This program sets up and runs an OpenMM simulation in a user-friendly way. It is roughly equivalent to to grompp/mdrun in Gromacs, dynamic in Tinker, and pmemd in Amber.
Some nice features include:
1) Extensive validation of options and checking dependencies / conflicts between options.
2) Reports your simulation progress, including speed in ns/day and time left.
3) You may use units from simtk.unit on the command line when specifying options with physical units.
4) Suggestions are provided for typos on the command line.
5) Restart files that contain state information (coordinates, velocities, and unit cell vectors) from the previous run.