runtype¶

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:

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

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

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

Todo

The dynamics part of the PB-(S)AM code should be moved out of the ELEC section. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/500