Skip to content

Latest commit

 

History

History
171 lines (95 loc) · 3.54 KB

parameters.rst

File metadata and controls

171 lines (95 loc) · 3.54 KB
Raw

Input Parameters

General Parameters

.. object:: structure (str)

   :optional: No

   The input filename in Protein Data Bank or GROMACS formats


.. object:: ncpus (int)

   :optional: No

   Number of CPUs to use in the calculations


.. object:: ionicstr (float)

   :optional: No

   Ionic strength of the medium


.. object:: ffinput='GROMOS' (str)

   :allowed values: ('GROMOS', 'AMBER', 'CHARMM')

   Forcefield of the input :py:data:`structure`. GROMOS is
   also valid for experimentally obtained strucutures


.. object:: ffID='G54a7' (str)

   :allowed values: ('G54A7')

   For the time being, only GROMOS54a7 based charged and radii are
   allowed.  In the future more forcefields will be added.



.. object:: sites='all' (str)

   CLI Syntax:
   sites_A  = all
   sites_A  = 1N, 18, 35, 48, 66, 129C

   API Syntax:
   sites = 'all'
   sites = {'A': ('1N', '18', '35', '48', '66', '129C')}
   Titration(parameters, sites=sites)


.. object:: clean_pdb=True (boolean)

   The input :py:data:`structure` files are preprocessed with
   PDB2PQR. To skip this step set :py:data:`clean_pdb` to False.

   CLI Syntax: yes or no

Poisson-Boltzmann Parameters

.. object:: epsin (float)

   :optional: No

   Internal dielectric to be used in the PB calculations.


.. object:: pbc_dimensions (int)

   :optional: No
   :allowed values: (0, 2)

   Number of dimensions with periodic boundaries. Use 0 for solvated
   proteins and 2 for lipidic systems.


.. object:: gsize=81 (int)

   DelPhi number of grid points per side of the cubic lattice.


.. object:: epssol=80.0 (float)

   Solvent dielectric to be used in the PB calculations.


.. object:: relpar=0.75 (float)

   DelPhi relaxation parameter in non-linear iteration convergence process.


.. object:: relfac=0.75 (float)

   DelPhi spectral radius.


.. object:: nonit=0 (float)

   DelPhi number of non-linear iterations.


.. object:: nlit=500 (float)

   DelPhi number of linear iterations.


.. object:: convergence=0.01 (float)

   DelPhi convergence threshold for maximum change of potential.


.. object:: scaleM=4 (float)

   DelPhi reciprocal of one grid spacing for the finer grid.


.. object:: scaleP=1 (float)

   DelPhi reciprocal of one grid spacing for the coarse grid used in the focusing step.


.. object:: slice=0.05 (float)

   Only used when :py:data:`pbc_dimensions` is 2. Fraction of the
   exterior of the lipid bilayer to be replicated with periodic
   boundary conditions.


.. object:: pbx=False (boolean)

   DelPhi periodic boundary conditions for the x edge of the grid


.. object:: pby=False (boolean)

   DelPhi periodic boundary conditions for the y edge of the grid


.. object:: bndcon=4 (int)

   :allowed values: (1, 2, 3, 4)

   DelPhi type of boundary condition.

   1. Zero
   2. Dipolar
   3. Focusing
   4. Coulombic


.. object:: precision='single' (str)

   :allowed values: ('single', 'double')

   Precision of the compiled DelPhi version being used.

Monte Carlo Parameters

.. object:: seed (int)

   Seed for the MC random generator


.. object:: pH='0,14' (str)

   pH value of the calculation. It can be a single value or a range.

   CLI syntax:

   pH = 0, 14


   API syntax:

   'pH': '0, 14'



.. object:: pHstep=0.25 (float)

   In case a pH range was provided :py:data:`pH`, the pH step of said
   range is :py:data:`pHstep`