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5.6. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS

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5.7. GRO file format — MDAnalysis.coordinates.GRO

Classes to read and write Gromacs GRO coordinate files; see the notes on the GRO format which includes a conversion routine for the box.

class MDAnalysis.coordinates.GRO.GROReader(grofilename, convert_units=None, **kwargs)

Now reads in velocities as well, if available.

Writer(filename, **kwargs)

Returns a CRDWriter for filename.

Arguments :
filename

filename of the output GRO file

Returns :

GROWriter

class MDAnalysis.coordinates.GRO.GROWriter(filename, convert_units=None, **kwargs)

GRO Writer that conforms to the Trajectory API.

Note

The precision is hard coded to three decimal places and velocities are not written (yet).

Set up a GROWriter with a precision of 3 decimal places.

Arguments :
filename

output filename

convert_dimensions_to_unitcell(ts)

Read dimensions from timestep ts and return appropriate unitcell

fmt = {'box_orthorhombic': '%10.5f%10.5f%10.5f\n', 'box_triclinic': '%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n', 'numatoms': '%5d\n', 'xyz': '%5s%-5s%5s%5s%8.3f%8.3f%8.3f\n', 'xyz_v': '%5s%-5s%5s%5s%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n'}

format strings for the GRO file (all include newline); precision of 3 decimal places is hard-coded here.

write(selection, frame=None)

Write selection at current trajectory frame to file.

Arguments :
selection

MDAnalysis AtomGroup (selection or Universe.atoms) or also Universe

Keywords :
frame

optionally move to frame number frame

The GRO format only allows 5 digits for resid and atom number. If these number become larger than 99,999 then this routine will chop off the leading digits.

Changed in version 0.7.6: resName and atomName are truncated to a maximum of 5 characters