MD NAMD

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy France
• Galaxy Europe
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["System Setup"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["Energy Minimizer"];
  2 -->|setup_crd| 3;
  2 -->|setup_psf| 3;
  2 -->|structure_prm| 3;
  4["NAMD MD Simulator NVT"];
  3 -->|pdbout| 4;
  3 -->|pmespec| 4;
  3 -->|xplorpsfout| 4;
  3 -->|bbrmsd| 4;
  3 -->|scrmsd| 4;
  3 -->|subsrmsd| 4;
  2 -->|structure_prm| 4;
  5["NAMD MD Simulator NPT"];
  3 -->|pdbout| 5;
  3 -->|pmespec| 5;
  3 -->|xplorpsfout| 5;
  4 -->|coorout| 5;
  4 -->|velout| 5;
  4 -->|xscout| 5;
  2 -->|structure_prm| 5;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows