Analysis using MDAnalysis
1.0

Workflow Type: Galaxy

Analysis of MD trajectories using MDAnalysis, generating a Ramachandran plot and various timeseries.

Associated Tutorial

This workflows is part of the tutorial Analysis of molecular dynamics simulations, available in the GTN

Features

Thanks to...

Workflow Author(s): Chris Barnett

Tutorial Author(s): Christopher Barnett, Tharindu Senapathi, Simon Bray, Nadia Goué

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
DCD input #main/DCD input DCD input
  • File
PDB input #main/PDB input PDB input
  • File

Steps

ID Name Description
2 RDF Analysis toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf/0.19
3 Cosine Content toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.19
4 Ramachandran Plots toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot/0.1.3
5 Distance Analysis toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_distance/mdanalysis_distance/0.19
6 Dihedral Analysis toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_dihedral/mdanalysis_dihedral/0.19

Outputs

ID Name Description Type
Cosine Content plot #main/Cosine Content plot n/a
  • File
Cosine Content raw data #main/Cosine Content raw data n/a
  • File
Dihedral Analysis plot #main/Dihedral Analysis plot n/a
  • File
Dihedral Analysis raw data #main/Dihedral Analysis raw data n/a
  • File
Distance Analysis plot #main/Distance Analysis plot n/a
  • File
Distance Analysis raw data #main/Distance Analysis raw data n/a
  • File
RDF Analysis plot #main/RDF Analysis plot n/a
  • File
RDF Analysis raw data #main/RDF Analysis raw data n/a
  • File
Ramachandran Plot #main/Ramachandran Plot n/a
  • File
Ramachandran Plot raw data #main/Ramachandran Plot raw data n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 11:04 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 11:04

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