Workflows

These workflows are associated with Running molecular dynamics simulations using GROMACS

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.

GROMACS Training Workflow

Last updated Oct 3, 2020

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy Main Galaxy France Galaxy Europe 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;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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:

Video: Importing a workflow from URL