Teacher’s guide to using SAMSON as a learning tool in high school


SAMSON is a desktop application for molecular modeling that is available for Windows, Linux and Mac at SAMSON Connect.

In this guide, you will find activities that can be performed with high school students in physics, chemistry and biology classes using SAMSON.

This guide starts with a couple of tutorials about SAMSON to feel at ease with the software, followed by two tutorials on elementary chemistry. After becoming sufficiently autonomous in SAMSON, there are two possible paths to choose from. One either proceeds to specialize in nanocarbons, working on nanotubes and other classic nanocarbon structures, or one may further explore the exciting world of proteins – visualizing and understanding their structure.





Introduction to SAMSON






These tutorials will give the students a short introduction on how to use SAMSON and a lot of its features. They will also learn the basic principles of a simulator.

-> “First steps on Samson

  • Keywords: Introduction, interface, atom creation, bond creation, simulation
  • Estimated time: 30 minutes

-> “Open and manipulate bigger molecules”

  •  Keywords: File manipulations, nanocar, nanostructure manipulation, simulation
  • Estimated time: 20 minutes











If you want to teach your students about chemistry notions, we suggest you do the two following tutorials. These will show you the different covalent bonds and how they change the shape of the molecules, as well as the concept of molecular conformations.

-> “Double, triple bonds”

  • Keywords: bond representation, ethane, ethylene, energy minimum
  • Estimated time: 15-20 minutes

-> “Chair, Boat and Twist-Boat Conformation of Cyclohexanes and Glucose

  • Keywords: Cyclohexane, glucose, conformation, Fehling’s solution, energy minimum
  • Estimated time: 30 minutes











For those interested in the fascinating and constantly developing nanoscience.  We propose two introductory guides on nanocarbons. The first has a more general approach on the most common nanocarbon structures while the second one demonstrates some of the current applications.

 -> “Nanocarbons : Graphene, nanotube and fullrene”

  • Keywords: nanoscience, graphene, nanotube 
  • Elements: Graphene Sheet Creator, Nanotube Creator
  • Estimated time: 20 minutes

-> “Simulation of stocking different molecules in a nanotube

  • Keywords: nanotube, application, dihydrogen, hydrophobia
  • Estimated time: 15-20 minutes










It is essential in the medical field to be able to understand the protein mechanisms, since a large part of the living world are constituted of proteins. Visualisation is a crucial part of this understanding. 

-> “Proteins: visualisation”

  • Keywords: proteins, secondary structure, hydrogen bonds, DNA 
  • Elements: Hydrogen Bond Finder
  • Estimated time: 25 minutes

-> “Proteins: application”

  • Keyword: biological research, glucose oxidase, glucose, acceptor sites, enzymatic catalytic reaction
  • Elements: AutoDock Vina
  • Estimated time: 20 min



You can find the download link for SAMSON here, along with the installation guide here.

You can create your personal account if you wish to add extra elements (“elements” in SAMSON are what “apps” are for a smartphone), but we advise you to install SAMSON with the following username and license key : education@samson-connect.net / 381DC-65340-A49A1-83183-AC9CD on the computer your students will be using, as this account already contains all the elements needed.


This guide is part of an university project, made over five months by five students. It is in no way already finished, and if you wish to contribute, have any suggestions for future activities, or perhaps you have created a tutorial yourself, do not hesitate to visit the forum.


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