GROMACS Training Workflow
7.0

Workflow Type: Galaxy

Running molecular dynamics simulations using GROMACS

Associated Tutorial

This workflows is part of the tutorial Running molecular dynamics simulations using GROMACS, available in the GTN

Features

Thanks to...

Tutorial Author(s): Simon Bray

gtn star logo followed by the word workflows

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 (earliest) Created 2nd Jun 2025 at 11:02 by GTN Bot

Added/updated 4 files


Open master 9c96271
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Views: 48   Downloads: 4   Runs: 0

Created: 2nd Jun 2025 at 11:02

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