charmm
======

This option defines the implementation details of CHARMM force field.

.. contents::
   :local:

.. option:: parameters
  
   .. list-table::
      :stub-columns: 1
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      * - Value
        - One or more file names
      * - Default
        - None

  Give the CHARMM force field parameter file names (paths may be included). There can be more than one files:

  .. code-block:: bash
    :linenos:

     charmm
       parameters par_all35_ethers.prm /home/zhang/userdef/par_all35_proteins.prm   
     end

  Note that if the same term, say bond ``CT-CT``, appears in more than one parameter files, then the latter one will overwrite the previous ones.

.. option:: topology
  
   .. list-table::
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      :widths: 5 20
   
      * - Value
        - A file name
      * - Default
        - None

   Give the topology file name of the molecule in PSF format (path may be included).

.. option:: scaling14

   .. list-table::
      :stub-columns: 1
      :widths: 5 20
   
      * - Value
        - A real number
      * - Default
        - ``1.0``
   
   Define the scaling factor for electrostatic interactions of 1-4 term.

.. option:: rcutoff

   .. list-table::
      :stub-columns: 1
      :widths: 5 20
   
      * - Value
        - A real number
      * - Default
        - ``15.0``
    
   Define the distance in Angstrom to cutoff non-bonded interactions.

   If ``rswitch`` is larger than ``rcutoff``, switching function will not be used and no cutoff is applied on long range forces.	

.. option:: rswitch

   .. list-table::
      :stub-columns: 1
      :widths: 5 20
   
      * - Value
        - A real number
      * - Default
        - ``10.0``
   
   Define the distance in Angstrom to activate switching function.
   
   If ``rswitch`` is larger than ``rcutoff``, switching function will not be used and no cutoff is applied on long range forces.	

.. option:: use_PBC

   Turn on periodic boundary condition for the system. If this option is not present, the system will be a non-periodic, gas phase one. 

.. option:: Lbox

   .. list-table::
      :stub-columns: 1
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      * - Value
        - Three real numbers
      * - Default
        - ``0. 0. 0.``
    
   When ``use_PBC`` is present, this option gives the lattice lengths along X, Y, and Z direction in Angstrom. 

   .. code-block:: bash
     :linenos:

     charmm
       use_PBC
       Lbox 86 86 86
     end

   This creates a simulation box of 86 Angstrom x 86 Angstrom x 86 Angstrom.

.. option:: electrostatic

   .. list-table::
      :stub-columns: 1
      :widths: 5 20
   
      * - Value
        - ``Cutoff`` Cutoff scheme for gas phase or periodic systems.
      * -  
        - ``PME`` Particle mesh Ewald (PME) method. Only available for periodic systems.
      * - Default
        - ``Cutoff``

   Assign the scheme to calculate electrostatic interaction. 
    
   For gas phase, ``Cutoff`` is the only possible way. For periodic systems, it is recommended to use ``PME``.

.. option:: PMEk
  
   .. list-table::
      :stub-columns: 1
      :widths: 5 20
   
      * - Value
        - Three integers
      * - Default
        - ``64 64 64``

   Assign the number of grids for PME long range force calculations. It is recommended that the number should be chosen as an integer close to the lattice length while is a multiply of only 2,3 and/or 5. For example, if ``Lbox`` is ``109. 109. 77``, then ``PMEk`` can be set to ``108 108 80``.