Max Linke edited this page Jun 4, 2017 · 1 revision

MDAnalysis v0.16.1 release!

release date: 06/03/17



  • Universe now works with StringIO objects for topologies and trajectories.
  • Residues with the same residue ids are not merged by default now (apply to PDB, GRO) (Issue #1306)
  • Improved print to screen format in waterdynamics module (using ProgressMeter).
  • PQRParser now treats insertion codes properly (Issue #1317)
  • made online docs responsive with the Alabaster Sphinx theme (#378)


  • In Universe.transfer_to_memory(): dt is now adjusted with step (Issue #1310)
  • Various documentation sphinx errors (PR #1312)
  • Bugfix in confdistmatrix.get_distance_matrix; now works on all trajectory types. (issue #1324)
  • Fixed bug "no molecules in water selection" in waterdynamics analysis module.
  • Fix hbond_analysis cannot deal with Universe where no two atoms are with 3A. (PR #1325)
  • Fix PDBParser docs for conect (issue #1246)
  • Fixed bug where amber topology files would fail to load if number of atoms was exactly divisible by number of atoms per line (issue #1331)
  • Fixed incorrect handling of residue names with trailing numbers in HydrogenBondAnalysis (issue #801)
  • Fixed AnalysisBase class provides numerical start,stop,step values (PR #1340)
  • Fixed PSFParser not creating multiple residues for identical resids in different segments. (Issue #1347, PR #1348)
  • Add the OC1 and OC2 from amber99sb-ildn to hydrogen bond acceptors (issue #1342)
  • Fix RMSF run return value (PR #1354)
  • Fixed documentation in pca (Issue #1378 PR #1379)


  • Enable various pylint warnings to increase python 3 compatibility
  • Change Mathjax cdn (Issue #1313)
  • Change mass_weight to weights for PSA analysis
  • Move mass_weights deprecation to version 0.18
  • Docs moved to (Issue #1315) and made responsive (Alabaster theme with readable-sphinx CSS) (Issue #378)
  • speed improvements parsing PDB / PDBQT / PQR / XYZ coordinate reader (Issue #1308)


utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma, richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst, kaceyreidy

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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