diff — APBS-PDB2PQR 1.6 documentation

# 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