GROMACS Training Workflow

computational-chemistry-md-simulation-gromacs/main-workflow

Author(s)

version Version
7
last_modification Last updated
Oct 3, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
computational-chemistry

Features

Tutorial
hands_on Running molecular dynamics simulations using GROMACS

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00035
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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

Input Label

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0 Get PDB file
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 Search in textfiles
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.2+galaxy0 GROMACS structure configuration
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0 GROMACS simulation MD simulation

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.2+galaxy0 View in ToolShed

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

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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
7 3ae7a9ecf 2020-10-03 01:23:46 gromacs
6 5f5f0c617 2020-07-27 09:23:46 Update main_workflow.ga
5 667ff3de9 2020-01-22 10:59:29 annotation
4 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
3 faf6d298a 2019-12-12 13:02:33 unflatten workflows
2 84d04eb28 2019-10-22 21:31:15 Update gromacs tutorial after changes to tools (#1635)
1 be6fece7f 2019-05-04 09:37:46 Simonbray compchem (#6)

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