Using the Amsterdam Modeling Suite in HPC systems

The Amsterdam Modeling Suite (AMS) features a set of modules that cover a wide range of simulations at different scales in computational chemistry and materials science: from quantum mechanics to fluid thermodynamics. Learn how to use this powerful tool for running large simulations on a supercomputer.

Verschillende iconen met focus op icoon training
10 Feb 2021

In this course you will be able to:

  • experience the basic use of the graphical user interface of AMS on your laptop with different applied systems
  • enhance your computations by using AMS on the supercomputing systems at SURF
  • understand how to exploit the best performance in your simulations
  • choose your preferred topic for the last session!

This workshop is organized in collaboration with the developers of AMS from the SCM company and an expert in the field of computational chemistry, Dr. Remco Havenith from the Rijksuniversiteit Groningen.


9:00-9:30 Overview of the Amsterdam Modeling Suite
9:30 - 11:30 Hands-on exercises on your laptop (e.g., building molecules, creating surfaces, optimizing structures, reactive molecular dynamics)
11:30-12:00 Introduction to the use of supercomputers and connection to SURF systems
12:00-13:00 Lunch break
13:00-13:30 Running small calculations on general HPC systems
13:30-14:30 A real-life case: (TD)DFT calculations with AMS
14:30-18.00 Advanced use cases on HPC systems: choose your topic!

At registration, please indicate which topic of interest you would like to have during the last session:

  1. QM/MM
  2. TD-DFTB
  3. Reaction paths and transition states
  4. Energy decomposition analysis
  5. Ground state periodic systems in chemistry

For whom?

Anyone interested in learning how to perform different simulations efficiently with the Amsterdam Modeling Suite in a supercomputing environment.


  • Basic knowledge of the Unix shell is necessary. If you are not familiar with it, please take a look at the shell tutorial from the Carpentries.
  • Your own laptop with a terminal emulator and a pre-installed version of AMS.
  • For Windows users we recommend to use MobaXterm (portable version) as terminal emulator.
  • Further details on the installation of AMS in your laptop will follow after registration.