diff¶

Specify the diffusion coefficients for each molecule in the system for a PB-(S)AM Brownian dynamics calculation.

diff {type} {dTrans} {dRot}

type

a string indicating the molecule dynamics type

stat
Stationary.
rot
Object is fixed but rotates
move
Object moves and rotates.
dTrans
Translational diffusion coefficient in units of Å2 ps-1. Used only with the move keyword.
dRot
Rotational diffusion coefficient. Used with the move and rot keywords.

Todo

What are the units for dRot? Documented as https://github.com/Electrostatics/apbs-pdb2pqr/issues/486

Note

The order of these keywords is expected to be identical to the order of the molecules in the READ section.

Todo

Add a mol id flag rather than have an implicit ordering of the diff keywords. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/487