GROMACS Training Workflow
computational-chemistry-md-simulation-gromacs/main-workflow
Launch in Tutorial Mode
question
galaxy-download Download
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 |
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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
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