CP/MM Tutorial

software (MOLDEN, CPMD, VMD, Gaussian09, Amber, GROMOS, etc) in order to
let you taste the everyday working in the biophysical field.
The procedure can be summarized in the following steps:
1. Calculate the dipole moment D v of acetone in vacuum
2. Perform a QM/MM molecular dynamics simulation for the acetone in a
classical water box at room temperature.
3. Calculate the dipole moment D for some random snapshots of this simulation
and take the mean value
4. Calculate the difference D - D v
Each file mentioned in this tutorial (in bold) can be found on the Aachen
supercomputer in the folder:
/home/ei250498/Tutorials/ACETONE
under the subfolder whose name starts with the number of the corresponding section
of this tutorial.
To do your tests and exercises, work in your own folder in $WORK filesystem by
creating a folder there by the command:
Then to go to your folder:
mkdir $WORK/QMMM_Tutorial
cd $WORK/QMMM_Tutorial
1 - Where to start?
Acetone is the organic compound with the formula (CH3) 2 CO. This colorless, mobile,
flammable liquid is the simplest example of the ketones:
Figure 1. Acetone
To obtain an initial structure we use the MOLDEN program. 1 As for all the programs
mentioned in this tutorial, the first time in each session you want to use molden you
need to initialize the environment in order to be able to recall it. This can be done
with a “source” command:
source /home/ei250498/PROGRAMS/MODULES/molden.sh
1 http://www.cmbi.ru.nl/molden/molden.html
2 An online general guide for the ZMAT Editor can be found at the web address: