diff

Todo

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

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 Ų 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/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/issues/487