Indicate what type of calculation you would like to run with the PB-(S)AM model.

runtype {type}

where type is the type of calculation to be perfomed:

Compute and print out the interaction energies, forces and torques on each molecule.
Print the electrostatic potential of points in the system.

Perform a Brownian Dynamics simulation, using forces and torques generated from the PB-(S)AM model. The calculation of force and torque has been integrated into a Brownian dynamics scheme that is detailed in Yap EH, Head-Gordon TL (2013) This option will generate a series of files of the form

The starting configuration of the system for the first trajectory
A file that prints how each trajectory was terminated and the time that this occurred at.
A VMD-readable xyz file for the trajectory of traj.
A file with positions, forces and torques for the system.


The dynamics part of the PB-(S)AM code should be moved out of the ELEC section. Documented in