Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows
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roles Set correct default Python Feb 8, 2018
.gitignore Also perform packer syntax check. May 25, 2016
.travis.yml Prep 1.4.3 Feb 9, 2018
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LICENSE Added LICENSE and doi Jan 28, 2016 Bump to 1.4.1 Nov 12, 2017
packer.json Bump to 1.4.1 Nov 12, 2017
playbook.yml Make Python 2 the default Feb 7, 2018

3D e-Chem Virtual Machine

Build Status DOI

Scripts to create a Vagrant box using packer and ansible.

For available software/datasets/workflows inside Virtual machine see


Create a new directory and cd to it then start virtual machine with

vagrant init nlesc/3d-e-chem
vagrant up

Usage screencast on YouTube:

3D-e-Chem Virtual Machine screencast on YouTube



packer build packer.json


Add box to Vagrant with

vagrant box remove --force --all nlesc/3d-e-chem
vagrant box add --name nlesc/3d-e-chem --force

Then use steps described at Usage chapter in a new directory.



Publish box on using the following steps:

  1. Create a new version
  2. Create a new provider
  3. Choose virtualbox as provider
  4. Choose Upload
  5. Press Continue to upload
  6. Upload the file generated by vagrant package
  7. Edit version
  8. Press Release version


Please see


When using 3D-e-Chem-VM please cite one of the following:

  • Zenodo software release DOI
  • R. McGuire, S. Verhoeven, M. Vass, G. Vriend, I. J. P. De Esch, S. J. Lusher, R. Leurs, L. Ridder, A. J. Kooistra, T. Ritschel, C. de Graaf (2017). 3D-e-Chem-VM: Structural cheminformatics research infrastructure in a freely available Virtual Machine. Journal of Chemical Information and Modeling. doi: