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