Oliver Beckstein edited this page Sep 26, 2015 · 3 revisions



  • multithreaded distance_array() (Issue 80, experimental); see the new core.parallel.distance module
  • MDAnalysis.analysis.rms for simple RMSD analysis
  • format of input coordinates can be set as (filename, format) tuples (Issue 76)
  • new AtomGroup.asphericity() and AtomGroup.shapeParameter() methods to compute shape descriptors.
  • access to forces (AtomGroup.forces with get_forces() and set_forces(); the default unit for force is kJ/(mol*A) and it is automatically converted from/to native). Currently, only the TRR Reader/Writer support forces.
  • all element masses
  • logger reports current version when starting


  • fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
  • fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
  • fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
  • fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
  • fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
  • Issue 122 (made installation of netCDF4 library optional, which means that users of the AMBER netcdf Reader/Writer will have to manually install the library and its dependencies netcdf and HDF5, see the wiki page on netcdf)


danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi

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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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