Richard Gowers edited this page Oct 10, 2015 · 2 revisions


  • Sean Seyler's Path Similarity analysis module got many more features. Check out the tutorial
  • Parsing of TPR files was vastly improved, including supporting v5.0+ of Gromacs thanks to Jonathan Barnoud
  • The installation process has been improved, any various minor annoyances removed, credit to Max Linke


API Changes

  • PrimitivePDBReader now imports occupancies into the TimeStep object. (Issue #396)
  • Atoms without a Universe now return NoDataError instead of AttributeError
  • AtomGroups of zero length or containing Atoms with no Universe raise a NoDataError when trying to access Universe
  • Atoms now keep a strong reference to Universe, meaning they do not become orphaned when the Universe goes out of scope (Issue #297)


  • Atom and AtomGroup now expose occupancy value as occupancy and occupancies properties (Issue #396)
  • XYZReader now supports frame indexing (Issue #428)
  • Reader objects can now be sliced using lists and arrays of indices (Issue #437)
  • PSAnalysis now includes Hausdorff pairs analysis and associated nearest neighbor plotting method (Issue #438)
  • New class PSAPair added to MDAnalysis.analysis.psa for handling Hausdorff pairs analysis (Issue #438)
  • PSAnalysis can now generate annotated heat maps (Issue #438)
  • Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
  • Additional getters added to Path and PSAnalysis (Issue #438)
  • MSD matrix function now globally available in MDAnalysis.analysis.psa (Issue #438)
  • Function for obtaining coordinate axes from numpy trajectories now globally available in MDAnalysis.analysis.psa (Issue #438)
  • TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
  • now looks for some configuration values in a config file. Each config option can also be changed via environment variables if they are prefixed with 'MDA_'. Current options are 'use_cython', 'use_openmp', 'debug_cflags'


  • An AtomGroup with 0 atoms now yields an IndexError on call to AtomGroup.write (Issue #434)
  • PSA changed to PSAnalysis to reduce namespace clutter (Issue #438)
  • To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'


  • Fixed minor issue in lib.mdamath.make_whole where if all bonds were correctly sized, it wouldn't notice that multiple fragments had been given. (Issue #445)
  • Fixed issue with PDB Topology parsing where if serials went over 100k, they wrapped to '***', breaking the parser (Issue #446)
  • Fixed AtomGroup.sequence() (Issue #451)
  • Fixed PrimitivePDBParser not detecting when resids had looped over 10,000. The original resid is stored as Atom.resnum (Issue #454)
  • Fixed TPR topology parser to treat all bonded interactions available in Gromacs 5.1 (Issue #222 and #352, pull request #463).


kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud

Project Information

GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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