A tool to run molecular dynamics workflows.

1403 commits | Last update: April 16, 2019

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What MDStudio can do for you

  • Molecular dynamics workflow creation and execution for biochemists
  • Micro-service based workflow management system
  • Flexible, interactive workflow execution locally or on HPC
  • Support for ATB, Gromacs, PLANTS, Paradocks, and many other tools

MDStudio provides biochemistry researchers in science and industry with the easiest and most flexible solution to running molecular dynamics-based workflows. It is community-developed open source software.

Read more
  • Real time data analysis
  • High performance computing
  • Workflow technologies
Programming Language
  • Python
  • Apache-2.0
Source code

Participating organizations


10 Presentations

  • MDStudio, microservice based molecular dynamics workflows
  • Presentation at National eScience Symposium
  • Presentation - NWO CHAINS 2016
  • Presentation - Dutch MD Days
  • Presentation - AIMMS Annual Meeting
  • Presentation - Automation in Biomolecular Simulations and Modelling
  • Presentation - FIGON Dutch Medicines Days
  • Presentation at 21st European Symposium on Quantitative Structure-Activity Relationship
  • Presentation - IXA Science and Innovation Award 2017
  • Presentation - National eScience Symposium 2017


  • Felipe Zapata
    Netherlands eScience Center
  • Marc van Dijk
    VU University Amsterdam
  • Paul Visscher
    Zefiros Software
  • Mick van Duijn
    Zefiros Software
Contact person
Marc van Dijk
VU University Amsterdam