6.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS

Resources: the GMS output format is a common output format for different GAMESS distributions: US-GAMESS, Firefly (PC-GAMESS) and GAMESS-UK.

Current version was approbated with US-GAMESS & Firefly only.

There appears to be no rigid format definition so it is likely users will need to tweak the GMSReader.

class MDAnalysis.coordinates.GMS.GMSReader(outfilename, **kwargs)

Reads from an GAMESS output file

Data:

ts

Timestep object containing coordinates of current frame

Methods:

len(out)

return number of frames in out

for ts in out:

iterate through trajectory

Note

GMSReader can read both uncompressed (foo.out) and compressed (foo.out.bz2 or foo.out.gz) files; decompression is handled on the fly

Changed in version 0.11.0: Frames now 0-based instead of 1-based. Added dt and time_offset keywords (passed to Timestep).

close()

Close out trajectory file if it was open.

property n_atoms

number of atoms in a frame

property runtyp

RUNTYP property of the GAMESS run

units = {'length': 'Angstrom', 'time': 'ps'}

dict with units of of time and length (and velocity, force, … for formats that support it)