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FAIRmat Tutorial 7: Molecular Dynamics Trajectories and Workflows in NOMAD

Watch the whole tutorial in our playlist on YouTube.

Preparation for the tutorial

  1. If you do not already have a NOMAD account, register for one here: https://nomad-lab.eu/prod/v1/staging/gui/about/information.
  2. Download the materials for tutorials 1 and 2 (linked below).
  3. Each of the downloaded directories will contain a “data“ folder with a zip file. Login to NOMAD at https://nomad-lab.eu/prod/v1/staging/gui/about/information and then go to Publish->Uploads at the top left of the page. For each zip file, click the “Create a new upload” button and then drag and drop the zip file (or click the “Click or drop files” button to navigate to the file via your file system). Once the processing is complete, you can rename this upload at the top left of the page using the pencil icon next to “unnamed upload” to better keep track for use during the tutorial.

Note that there is no preparation necessary for tutorial 3. However, you are free to peruse the notebooks in advance.

Materials

Session Materials

Introduction to FAIRmat and NOMAD
Luca Ghiringhelli 

Video

Slides

 

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

Video

Notes (pdf)

Notes, exercise materials and solutions

Guided Tutorial 2: Molecular dynamics overview page and workflow visualizer
Joseph Rudzinski

Video

Notes (pdf)

Notes, exercise materials and solutions

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

Video

Notes, exercise materials and solutions

Whole tutorial Video playlist