runtypeΒΆ
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 - ELECsection. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/500