solvate
========================

.. contents::
  :local:

This task is used to build a water box around the input molecule.

Arguments
-------------

.. option:: -i, --in

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - Yes
    * - Argument
      - PDB filename or XYZ filename
    * - Default
      - None
  
  Give the input molecule.

.. option:: -t, --top

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - Yes
    * - Argument
      - PSF filename
    * - Default
      - None
  
  Give the input topology.

.. option:: -o, --out

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - A filename prefix
    * - Default
      - None
  
  Give the output filename prefix. If not given, the molecule and topology will be written to ``x-solvate.pdb`` and ``x-solvate.psf``, respectively.

.. option:: --box

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - Yes
    * - Argument
      - Three real numbers: x, y, z in Angstrom
    * - Default
      - None
  
  Give the box size in Angstrom.

.. option:: --charge

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - An integer.
    * - Default
      - ``0``

  Give the target total charge of the system after adding ions. If not given, pdbtop will neutralize the system by adding counter ions (NaCl).

.. option:: --ionic-strength

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - A real number in mol/L
    * - Default
      - ``0.01``

  Give the target ionic strength of the system after adding ions. If not given, pdbtop will set the ionic strength to ``0.01`` mol/L by adding counter ions (NaCl).
  
.. option:: --no-add-ions

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - None
    * - Default
      - None
  
  By default, pdbtop will add ions (NaCl) to the system. But if ``--no-add-ions`` is given, this will not be done.

.. option:: --droplet

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - None
    * - Default
      - None
  
  If this is given, pdbtop will generate a droplet instead of box.
  
.. option:: --move

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - Three real numbers: x, y, z in Angstrom
    * - Default
      - None
  
  Move the center of box or droplet size in Angstrom.

These are 2 examples:
  
.. code-block:: bash
  
  # Solavte the system in a water box of 70x70x70 Angstrom^3 with default ionic strength (0.01 mol/L)
  $ pdbtop.exe solvate -i 5vbm-92v-2.pdb -t 5vbm-92v-2.psf -o 5vbm-sol --box "70 70 70" 

.. code-block:: bash
  
  # Solavte the system in a water box of 70x70x70 Angstrom^3 with ionic strength 0.02 mol/L
  $ pdbtop.exe solvate -i 5vbm-92v-2.pdb -t 5vbm-92v-2.psf -o 5vbm-sol --box "70 70 70" --ionic-strength 0.02