FAIRmat Tutorial 7: Molecular Dynamics Trajectories and Workflows in NOMAD


The FAIRmat consortium is committed to extending the NOMAD infrastructure to a wide variety of materials science data. To support soft matter simulations (e.g., atomistic molecular dynamics simulations), a number of challenges arise, primarily due to the volume and variety of data. The FAIRmat team is working to overcome these challenges, and the NOMAD infrastructure is now equipped with new metadata, features, and tools specifically designed to ease the FAIR treatment of trajectory data and workflows. Parsers have been implemented for two of the most popular molecular dynamics codes (Gromacs and Lammps), with plans for quick expansion to additional codes within the next year. The NOMAD Metainfo now describes the system’s hierarchical structure (in terms of bond topology) through the concept of fixed chemical bonds defined within classical force fields. The NOMAD GUI provides a bespoke overview page for molecular dynamics data, which includes tools that ease visualization of the system topology and automatically displays structural, dynamic, and thermodynamic observables that can assist in a fast assessment of system equilibration. Additionally, a native workflow visualizer allows the user to connect individual simulation entries into complex workflows. Finally, the NOMAD Python module facilitates custom trajectory analysis, for instance in a Jupyter notebook, with functions that convert a NOMAD archive entry to an instance of the MDAnalysis data class.

This tutorial invites both experienced and completely novice NOMAD users to learn about these new features for molecular dynamics trajectories. A brief introduction to the FAIRmat consortium and the NOMAD infrastructure will be given, followed by guided and interactive tutorials highlighting the various features described above


This tutorial will take place online on Wednesday February 15, 2023. All times are Central European Time=UTC+1

 This is an interactive guided tutorial. The exact timetable may be adjusted on the fly.

Time Session
14:00 - 14:30

Introduction to FAIRmat and NOMAD

Luca Ghiringhelli 


Guided Tutorial 1: Uploading molecular dynamics data and examining the metadata

Joseph Rudzinski

15:00 - 15:40

Guided Tutorial 2: Molecular dynamics overview page and workflow visualizer

Joseph Rudzinski

15:40 - 15:50


15:50 - 16:40

Guided Tutorial 3: Extracting data from the archive and trajectory analysis

Joseph Rudzinski

16:40 - 17:00


FAIRmat Area C Team