GROMACS Training Workflow

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Workflow Type: Galaxy

Running molecular dynamics simulations using GROMACS

Associated Tutorial

This workflows is part of the tutorial GROMACS Training Workflow, available in the GTN

Features

Thanks to...

Tutorial Author(s): Simon Bray

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1130?version=2

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
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
gro_output #main/gro_output n/a
  • File
xtc_output #main/xtc_output n/a
  • File

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 Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
The Protein Data Bank (PDB)
Gromacs
License
Creative Commons Attribution 4.0 International
Activity

Views: 181   Downloads: 80

Created: 25th Jun 2024 at 11:01

Last updated: 25th Jun 2024 at 11:01

help Attributions

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Total size: 117 KB
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