XYZ trajectory

Coordinate reader	MDAnalysis.coordinates.XYZ.XYZReader
Coordinate writer	MDAnalysis.coordinates.XYZ.XYZWriter
Topology parser	MDAnalysis.topology.XYZParser.XYZParser

The XYZ format is a loosely defined, simple coordinate trajectory format. The implemented format definition was taken from the VMD xyzplugin and is therefore compatible with VMD.

Reading in

As XYZ files only have atom name information, the atoms are all assigned to the same residue and segment.

The default timestep in MDAnalysis is 1 ps. A different timestep can be defined by passing in the dt argument to Universe.

XYZ specification

Definiton used by the XYZReader and XYZWriter (and the VMD xyzplugin from whence the definition was taken):

[ comment line            ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
[ N                       ] # of atoms, required by this xyz reader plugin  line 1
[ molecule name           ] name of molecule (can be blank)                 line 2
atom1 x y z [optional data] atom name followed by xyz coords                line 3
atom2 x y z [ ...         ] and (optionally) other data.
...
atomN x y z [ ...         ]                                                 line N+2

Note

• comment lines not implemented (do not include them)

• molecule name: the line is required but the content is ignored at the moment

• optional data (after the coordinates) are presently ignored