Module 2: Single Point Calculations at Quantum Mechanical

Level

Aditya Wibawa Sakti, D.Sc.

February 15, 2021

1 Introduction
This handout is made for introducing some basic Linux commands in a task-based mission. The
module contains the following: We are going to learn about how to calculate the total energy
of organic molecules without performing any geometry optimizations. At first, you will need to
make some organic molecules (at least 20 for each group) by using either smiles conversion or
Avogadro drawing software. I will recommend you to use the latter, in case you are not familiar
with the command line interface.

2 Structure Preparation
1. Open the Avogadro program by clicking the start menu button and click Avogadro.

2. Once you are there, draw any molecules. The molecule does not need to be a single
molecule, it can be dimer or any molecular systems. In this case, I am drawing a cy-
clopentane.

3. Once you finished, save your molecule in a Cartesian coordinate format (.xyz) by clicking
file → Save As....

4. Save your molecule as .xyz file in D:, C: disk, or in any folder that you can access from
both Ubuntu terminal and Windows Explorer.

5. Make other molecules in the same way. Each molecule has to be in a folder. For example,
I created cyclopentane.xyz and located it in cyclopentane folder. The group who can
make the most organic molecules will get the highest score in this exercise.

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3 Single Point Calculation at xTB Level
You created many organic molecules from the previous section. Now, we are going to learn
how to calculate the energy at the xTB level. I usually call this process as single point
calculation (SPC). Basically, in SPC, you only calculate the electronic energy of your system.
What is the meaning of the electronic energy?

1. Open your Ubuntu terminal by clicking the start menu and choose Ubuntu. In some cases,
it may have another name, e.g., Ubuntu 20.04, Ubuntu 18.04, etc.

2. Change directory into a directory where your molecule is located. In this case, I will go
to the cyclopentane folder by typing:

cd cyclopentane/

Depending on your folder location, you need to type it differently.

3. Once you get there, you may type ls and you will see your molecule as shown below:

4. Now, it is time to calculate the energy, you can just type:

xtb cyclopentane.xyz ¿ xtb.log

By typing the above command, it means that you are going to calculate the energy of
cyclopentane molecule and saving the whole information of the xtb outputs in xtb.log.

5. The calculation will finish in less than one second. If you have a larger molecule, it may
take minutes (Well, at least not hours).

6. Check the xtb.log by typing less xtb.log. You need to reach the end of the line by
pressing shift+G. To go to the beginning of the line, you can just press GG (pressing G
button twice).

7. You need to find three quantities, namely, total energy, gradient norm, and HOMO-
LUMO gap. In my case, those quantities are shown below:

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8. Make a table that consists of four columns, namely, Molecule, Total energy, gradient
norm, and HOMO-LUMO gap. You will use your molecules in the next lecture, then
please keep your folder and the calculated properties.

9. The last question, What is the meaning of Gradient norm in your calculation?