CP/MM Tutorial

Then, you can run molden by simply typing:
molden &
In the Molden Control panel at the right, deselect the “Shade” button and press on the
“ZMAT Editor” button that is a tool to create and/or manipulate structures on screen
and to optimize the structures on a force field level.
The use of the editor is rather intuitive. 2 In the following a synthetic list of the steps to
create the acetone molecule:
• Press “Add line”
• Select Carbon from the Periodic Table
• Press “Substitute atom by Fragment” and without releasing the mouse button
select the –HC=O
• Press “Add line”
• Select Hydrogen from the Periodic Table
• Click, in the Main screen, on the 4 atoms H,C,O,H in sequence to define the
connectivity of the new H atom in the molecule
• Highlight a Hydrogen by pressing on the atom in the Main screen or in the list
of atoms in Zmat Editor
• Press “Substitute atom by Fragment” and without releasing the mouse button
select the –CH3
• Do the same for the other Hydrogen
Then, we can save the structure in the xyz format by writing the name of the file in
the field “File name?”, choosing the “XYZ” format in the menu which appear when
you press on the square “Cartesian” at the right bottom and finally pressing “Write Z-
Matrix”.
Close the ZMAT Editor by clicking the “Close” button on the right top and then by
pressing on the button with a skull.
2 - Dipole moment in vacuum
We will use CPMD to calculate the dipole moment of acetone in gas phase.
To initialize the environment and be able to use CPMD:
source /home/ei250498/PROGRAMS/MODULES/cpmd.sh
Any program can be run interactively on the login node. In the following we report
the command to do that. However, if your job is supposed to run for more than 5
minutes this is NOT a good practice: longer jobs should be run on the computational
node by using the batch system. This can be accomplished by writing a simple batch
script where you insert the information about your job and then submit the request to
the batch system through the command:
2 An online general guide for the ZMAT Editor can be found at the web address:
http://www.cmbi.ru.nl/molden/zmat/zmat.html#add