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45 lines
1012 B
ReStructuredText
45 lines
1012 B
ReStructuredText
.. _diff:
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diff
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====
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Specify the diffusion coefficients for each molecule in the system for a PB-(S)AM Brownian dynamics calculation.
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.. code-block:: bash
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diff {type} {dTrans} {dRot}
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``type``
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a string indicating the molecule dynamics type
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``stat``
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Stationary.
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``rot``
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Object is fixed but rotates
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``move``
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Object moves and rotates.
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``dTrans``
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Translational diffusion coefficient in units of Å\ :sup:`2` ps\ :sup:`-1`.
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Used only with the ``move`` keyword.
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``dRot``
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Rotational diffusion coefficient.
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Used with the ``move`` and ``rot`` keywords.
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.. todo::
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What are the units for ``dRot``?
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Documented as https://github.com/Electrostatics/apbs-pdb2pqr/issues/486
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.. note::
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The order of these keywords is expected to be identical to the order of the molecules in the READ section.
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.. todo::
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Add a ``mol id`` flag rather than have an implicit ordering of the ``diff`` keywords.
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Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/487
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