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.. _old_write:
write
=====
.. currentmodule:: apbs.input_file.calculate
.. note::
This command has been ported to the *new APBS syntax* (see :ref:`new_input_format`); see :class:`generic.WriteMap` and specific functions for different calculations:
* Finite differences; see :func:`finite_difference.write_atom_potentials`.
* Finite elements; see :func:`finite_elements.write_atom_potentials`.
This controls the output of scalar data calculated during the Poisson-Boltzmann run.
This keyword can be repeated several times to provide various types of data output from APBS.
The syntax is:
.. code-block:: bash
write {type} {format} {stem}
``type``
A string indicating what type of data to output:
``charge``
Write out the biomolecular charge distribution in units of e\ :sub:`c` (electron charge) per Å\ :sup:`3` (multigrid only).
``pot``
Write out the electrostatic potential over the entire problem domain in units of k\ :sub:`b` T e\ :sub:`c`\ :sup:`-1` (multigrid and finite element), where
k\ :sub:`b`
Boltzmann's constant: 1.3806504 × 10\ :sup:`−23` J K\ :sup:`-1`
T
The temperature of your calculation in K
e\ :sub:`c`
is the charge of an electron: 1.60217646 × 10\ :sup:`-19` C
As an example, if you ran your calculation at 300 K, then the potential would be written out as multiples of
k\ :sub:`b` T e\ :sub:`c`\ :sup:`-1` = (1.3806504 × 10\ :sup:`−23` J K\ :sup:`-1`) × (300 K) × (1.60217646 × 10\ :sup:`-19` C)\ :sup:`-1` = (4.1419512 × 10\ :sup:`-21` J) × (6.241509752 × 10\ :sup:`18` C\ :sup:`-1`) = 25.85202 mV
``atompot``
Write out the electrostatic potential at each atom location in units of k\ :sub:`b` T e\ :sub:`c`\ :sup:`-1` (multigrid and finite element).
``smol``
Write out the solvent accessibility defined by the molecular surface definition (see :ref:`elecsrfm` ``smol``).
Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element).
``sspl``
Write out the spline-based solvent accessibility (see :ref:`elecsrfm` ``spl2``).
Values are unitless and range from 0 (inaccessible) to 1 (accessible) (multigrid and finite element)
``vdw``
Write out the van der Waals-based solvent accessibility (see :ref:`elecsrfm` ``smol`` with :ref:`srad` 0.0).
Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element)
``ivdw``
Write out the inflated van der Waals-based ion accessibility (see :ref:`elecsrfm` ``smol``).
Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element)
``lap``
Write out the Laplacian of the potential :math:`\nabla^2 \phi` in units of k\ :sub:`B` T e\ :sub:`c`\ :sup:`-1` Å\ :sup:`-2` (multigrid only).
``edens``
Write out the "energy density" :math:`-\nabla \cdot \epsilon \nabla \phi` in units of k\ :sub:`B` T e\ :sub:`c`\ :sup:`-1` Å\ :sup:`-2` (multigrid only).
``ndens``
Write out the total mobile ion number density for all ion species in units of M (multigrid only).
The output is calculated according to the formula (for nonlinear PB calculations): :math:`\rho(x) = \sum_i^N {\bar{\rho}_i e^{-q_i\phi(x) - V_i (x)}}`, where *N* is the number of ion species, :math:`\bar{\rho}_i` is the bulk density of ion species *i*, :math:`q_i` is the charge of ion species *i*, :math:`\phi(x)` is the electrostatic potential, and :math:`V_i` is the solute-ion interaction potential for species *i*.
``qdens``
Write out the total mobile ion charge density for all ion species in units of e\ :sub:`c` M (multigrid only).
The output is calculated according to the formula (for nonlinear PB calculations): :math:`\rho(x) = \sum_i^N {\bar{\rho}_i q_i e^{-q_i\phi(x) - V_i (x)}}`, where *N* is the number of ion species, :math:`\bar{\rho}_i` is the bulk density of ion species *i*, :math:`q_i` is the charge of ion species *i*, :math:`\phi(x)` is the electrostatic potential, and :math:`V_i` is the solute-ion interaction potential for species *i*.
``dielx`` or ``diely`` or ``dielz``
Write out the dielectric map shifted by 1/2 grid spacing in the {x, y, z}-direction (see :ref:`read_old_input` ``diel``).
The values are unitless (multigrid only).
``format``
A string that specifies the format for writing out the data:
``dx``
Write out data in :doc:`/formats/opendx`.
This is the preferred format for APBS I/O. (multigrid and finite element).
``avs``
Write out data in AVS UCD format. (finite element only).
``uhbd``
Write out data in :doc:`/formats/uhbd`. (multigrid only).
``gz``
Write out :doc:`/formats/opendx` in gzipped (zlib) compatible format.
Appends .dx.gz to the filename.
``flat``
Write out data as a plain text file. (multigrid and finite element).
``stem``
A string that specifies the path for the output; files are written to :file:`stem.{XYZ}`, where ``XYZ`` is determined by the file format (and processor rank for parallel calculations).
If the pathname contains spaces, then it must be surrounded by double quotes.
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