Workflow Type: Galaxy
Open
Frozen
Running molecular dynamics simulations using GROMACS
Associated Tutorial
This workflows is part of the tutorial GROMACS Training Workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Simon Bray
Steps
ID | Name | Description |
---|---|---|
0 | Get PDB file | toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0 |
1 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
2 | GROMACS initial setup | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.2+galaxy0 |
3 | GROMACS structure configuration | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.2+galaxy0 |
4 | GROMACS solvation and adding ions | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.2+galaxy0 |
5 | GROMACS energy minimization | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.2+galaxy0 |
6 | NVT equilibration | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0 |
7 | NPT equilibration | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0 |
8 | MD simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
gro_output | #main/gro_output | n/a |
|
xtc_output | #main/xtc_output | n/a |
|
Version History
7.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche
Added/updated 4 files
Open
master
8ee8cf3
8.0 (earliest) Created 25th Jun 2024 at 11:01 by Helena Rasche
Added/updated 4 files
Frozen
8.0
ed8b4b3
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
Creators
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Discussion Channel
Activity
Views: 181 Downloads: 80
Created: 25th Jun 2024 at 11:01
Last updated: 25th Jun 2024 at 11:01
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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