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2.6.1

Getting started

  • Installation
  • Quick start guide
  • Frequently asked questions
  • Examples
    • Quick start guide
    • Constructing, modifying, and adding to a Universe
    • Transformations
    • Other
      • Using ParmEd with MDAnalysis and OpenMM to simulate a selection of atoms
    • Alignments and RMS fitting
    • Distances and contacts
    • Trajectory similarity
    • Structure
    • Dimension reduction
    • Polymers and membranes
    • Volumetric analyses
  • API docs

Data structures

  • Universe
  • AtomGroup
  • Groups of atoms
  • Atom selection language
  • The topology system

Trajectories

  • Trajectories
  • Slicing trajectories
  • On-the-fly transformations
  • Units and constants

Input/output

  • Reading and writing files
  • Format overview
  • Guessing
  • Auxiliary files
  • Selection exporters
  • Format reference

Analysis

  • Analysis
  • Alignments and RMS fitting
  • Distances and contacts
  • Trajectory similarity
  • Structure
  • Volumetric analyses
  • Dimension reduction
  • Polymers and membranes
  • Hydrogen Bond Analysis
  • Writing your own trajectory analysis
  • Parallelizing analysis

Advanced

  • Standard residues in MDAnalysis selections
  • Advanced topology concepts
  • Example data

Contributing

  • Contributing to MDAnalysis
  • Contributing to the main codebase
  • Contributing to the user guide
  • Preparing a release
  • Module imports in MDAnalysis
  • Tests in MDAnalysis
  • Development docs
  • References
MDAnalysis User Guide
  • Examples
  • Other
  • View page source

Other

  • Using ParmEd with MDAnalysis and OpenMM to simulate a selection of atoms
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