Calculation of the structure, charges and vibrational frequencies of water

As an example of calculations of molecules for application to the parameterization of molecular force fields we will calculate the molecular properties of water using density functional theory. We will begin with a coordinate file. You can create a water molecule using the Builder in insightII. First enter InsightII by typing

Ø InsightII

at the command line. Invoke the Builder by selecting it from the menu that appears when you click on spiral icon on the upper left hand corner of the graphical user interface.

Use the Fragment/Get command to call up the fragment library. In the first set of available fragments you should see a water molecule. Select it. You should see a stick representation of a water molecule on the screen. Then you can close the fragment library. Now you can save the water molecule in a car (coordinate file) using the Molecule/Put command. Call it h2o.car.

To perform a DFT calculation using DMol3 you will need to copy the template.input file giving it the same root name as the car file.

Ø cp template.input h2o.input

Then edit the h2o.input file using the vi editor.

Ø vi h2o.input

Select optimize_frequency as the calculation type. Turn on calculation of Mulliken charges. You can also use electrostatic potential fitting if you want. This option is invoked by adding the text

esp_fit on

in the input file. You may put this text anywhere, but a convenient place is in the properties section just below Hirshfeld charge.

Set up the job and run the DFT calculation.