Tyler Reddy edited this page May 5, 2015 · 2 revisions


  • 0.6.3 release
  • minimum requirement is python 2.4 python 2.5 (using with_statement in the analysis module and we have not tested on 2.3 in a while)
  • requires Biopython (
  • analysis modules (MDAnalysis.analysis):
    • lipid bilayer leaflet detection
    • native contact analysis ("q1-q2")
    • rms-fitting based on sequence alignment
  • write selections for other codes from AtomGroups (VMD, pymol, CHARMM, Gromacs ndx)
  • gro reader (Issue 31)
  • better API for loading a topology and a coordinate file in Universe()
  • trajectory reader: DCDReader can reverse trajectory with negative step increment; XTC/TRRReader can do simple (forward) slices by doing (slow!) sequential iteration
  • deprecated principleAxes() and introduced principalAxes() with less confusing return values (Issue 33).
  • fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
  • added basic XYZ reader with compression support (Issue 35)
  • PDB reader guesses masses (unknown elements are set to 0)


orbeckst, denniej0, danny.parton, philipwfowler

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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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