Tutorial for Atomic Population and Charge Analysis

This short tutorial shows, how to perform a Mulliken and Löwdin population analysis with ORBKIT analytically, and how to write the output to an xyz or a PDB file.

Computation of the Atomic Populations and Charges

First, we have to import some modules and set some of ORBKITs options:

from orbkit import read, atomic_populations

Then, we have to read the input file:

# Open molden file and read parameters
qc = read.main_read('h2o.molden')

Now, we have to call the respective functions:

For a Mulliken Population Analysis:

pop = atomic_populations.mulliken(qc)

and for a Löwdin Population Analysis:

pop = atomic_populations.lowdin(qc)

The return value pop is a dictionary, which contains information about the population analysis and has following members:

Variable	Contents
population	Contains the population for each atom.
charge	Contains the charges for each atom.

Creation of an Output File

ORBKIT provides two possible output file formats for the population analysis: the PDB and the xyz file format:

from orbkit.output import pdb_creator,xyz_creator
# Write a PDB file
pdb_creator(qc.geo_info,qc.geo_spec,filename='charges',charges=pop['charge'],comments='')
# Write an xyz file
xyz_creator(qc.geo_info,qc.geo_spec,filename='charges',charges=pop['charge'],comments='')

This will write two files: charges.pdb and charges.xyz, which can be processed for visualization by several programs.

For instance, you can depict the PDB file containing the partial charges in VMD:

1. Load the file:

$ vmd -m charges.pbd

2. Go to Graphics->Representations
3. Select CPK as Drawing Method
4. Select Beta as Coloring Method