runtype — APBS-PDB2PQR 1.6 documentation

# 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