GROMACS Training Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["Get PDB file"];
  1["Search in textfiles"];
  0 -->|output| 1;
  2["GROMACS initial setup"];
  1 -->|output| 2;
  3["GROMACS structure configuration"];
  2 -->|output2| 3;
  4["GROMACS solvation and adding ions"];
  2 -->|output1| 4;
  3 -->|output| 4;
  5["GROMACS energy minimization"];
  4 -->|output2| 5;
  4 -->|output1| 5;
  6["NVT equilibration"];
  2 -->|output3| 6;
  4 -->|output2| 6;
  5 -->|output1| 6;
  7["NPT equilibration"];
  2 -->|output3| 7;
  4 -->|output2| 7;
  6 -->|output1| 7;
  6 -->|output5| 7;
  8["MD simulation"];
  4 -->|output2| 8;
  7 -->|output1| 8;
  7 -->|output5| 8;
  027305f5-213b-40af-8e2b-c376d5d2e294["Output\nxtc_output"];
  8 --> 027305f5-213b-40af-8e2b-c376d5d2e294;
  style 027305f5-213b-40af-8e2b-c376d5d2e294 stroke:#2c3143,stroke-width:4px;
  e745fd4c-f607-4215-84e4-c62587c8c07a["Output\ngro_output"];
  8 --> e745fd4c-f607-4215-84e4-c62587c8c07a;
  style e745fd4c-f607-4215-84e4-c62587c8c07a stroke:#2c3143,stroke-width:4px;

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-gromacs/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