7.8. 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.

7.8.1. Writing GRO files

By default any written GRO files will renumber the atom ids to move sequentially from 1. This can be disabled, and instead the original atom ids kept, by using the reindex=False keyword argument. This is useful when writing a subsection of a larger Universe while wanting to preserve the original identities of atoms.

For example:

>>> u = mda.Universe()`

>>> u.atoms.write('out.gro', reindex=False)

# OR
>>> with mda.Writer('out.gro', reindex=False) as w:
...     w.write(u.atoms)

7.8.2. Classes

class MDAnalysis.coordinates.GRO.GROReader(filename, convert_units=True, n_atoms=None, **kwargs)[source]

Reader for the Gromacs GRO structure format.

Note

This Reader will only read the first frame present in a file.

Note

GRO files with zeroed 3 entry unit cells (i.e. 0.0   0.0   0.0) are read as missing unit cell information. In these cases dimensions will be set to None.

Changed in version 0.11.0: Frames now 0-based instead of 1-based

Changed in version 2.0.0: Reader now only parses boxes defined with 3 or 9 fields. Reader now reads a 3 entry zero unit cell (i.e. [0, 0, 0]) as a being without dimension information (i.e. will the timestep dimension to None).

Writer(filename, n_atoms=None, **kwargs)[source]

Returns a CRDWriter for filename.

Parameters:

filename (str) – filename of the output GRO file

Return type:

GROWriter

units = {'length': 'nm', 'time': None, 'velocity': 'nm/ps'}

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

class MDAnalysis.coordinates.GRO.GROWriter(filename, convert_units=True, n_atoms=None, **kwargs)[source]

GRO Writer that conforms to the Trajectory API.

Will attempt to write the following information from the topology:

  • atom name (defaults to ‘X’)

  • resnames (defaults to ‘UNK’)

  • resids (defaults to ‘1’)

Note

The precision is hard coded to three decimal places.

Note

When dimensions are missing (i.e. set to None), a zero width unit cell box will be written (i.e. [0.0, 0.0, 0.0]).

Changed in version 0.11.0: Frames now 0-based instead of 1-based

Changed in version 0.13.0: Now strictly writes positions with 3dp precision. and velocities with 4dp. Removed the convert_dimensions_to_unitcell method, use Timestep.triclinic_dimensions instead. Now now writes velocities where possible.

Changed in version 0.18.0: Added reindex keyword argument to allow original atom ids to be kept.

Changed in version 2.0.0: Raises a warning when writing timestep with missing dimension information (i.e. set to None).

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

Parameters:

  • filename (str) – output filename

  • n_atoms (int (optional)) – number of atoms

  • convert_units (bool (optional)) – units are converted to the MDAnalysis base format; [True]

  • reindex (bool (optional)) – By default, all the atoms were reindexed to have a atom id starting from 1. [True] However, this behaviour can be turned off by specifying reindex =False.

Note

To use the reindex keyword, user can follow the two examples given below.:

u = mda.Universe()

Usage 1:

u.atoms.write('out.gro', reindex=False)

Usage 2:

with mda.Writer('out.gro', reindex=False) as w:
    w.write(u.atoms)
fmt = {'box_orthorhombic': '{box[0]:10.5f} {box[1]:9.5f} {box[2]:9.5f}\n', 'box_triclinic': '{box[0]:10.5f} {box[4]:9.5f} {box[8]:9.5f} {box[1]:9.5f} {box[2]:9.5f} {box[3]:9.5f} {box[5]:9.5f} {box[6]:9.5f} {box[7]:9.5f}\n', 'n_atoms': '{0:5d}\n', 'xyz': '{resid:>5d}{resname:<5.5s}{name:>5.5s}{index:>5d}{pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}\n', 'xyz_v': '{resid:>5d}{resname:<5.5s}{name:>5.5s}{index:>5d}{pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{vel[0]:8.4f}{vel[1]:8.4f}{vel[2]:8.4f}\n'}

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

units = {'length': 'nm', 'time': None, 'velocity': 'nm/ps'}

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

write(obj)[source]

Write selection at current trajectory frame to file.

Parameters:

obj (AtomGroup or Universe)

Note

The GRO format only allows 5 digits for resid and atom number. If these numbers 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

Changed in version 0.16.0: frame kwarg has been removed

Changed in version 2.0.0: Deprecated support for calling with Timestep has nwo been removed. Use AtomGroup or Universe as an input instead.

7.8.3. Developer notes: GROWriter format strings

The GROWriter class has a GROWriter.fmt attribute, which is a dictionary of different strings for writing lines in .gro files. These are as follows:

n_atoms

For the first line of the gro file, supply the number of atoms in the system. E.g.:

fmt['n_atoms'].format(42)
xyz

An atom line without velocities. Requires that the ‘resid’, ‘resname’, ‘name’, ‘index’ and ‘pos’ keys be supplied. E.g.:

fmt['xyz'].format(resid=1, resname='SOL', name='OW2', index=2, pos=(0.0, 1.0, 2.0))
xyz_v

As above, but with velocities. Needs an additional keyword ‘vel’.

box_orthorhombic

The final line of the gro file which gives box dimensions. Requires the box keyword to be given, which should be the three cartesian dimensions. E.g.:

fmt['box_orthorhombic'].format(box=(10.0, 10.0, 10.0))
box_triclinic

As above, but for a non orthorhombic box. Requires the box keyword, but this time as a length 9 vector. This is a flattened version of the (3,3) triclinic vector representation of the unit cell. The rearrangement into the odd gromacs order is done automatically.