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 movekeyword.
- dRot
- Rotational diffusion coefficient.
Used with the moveandrotkeywords.
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