runtype

Todo

This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).

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/issues/500