### Navigation

- index
- modules |
- next |
- previous |
- MDAnalysis 0.7.7 documentation »
- 5. Coordinates modules »

# 5.13. Gromacs XTC file IO — `MDAnalysis.coordinates.XTC`

Reading of Gromacs XTC trajectories.

See also

`MDAnalysis.coordinates.xdrfile.libxdrfile` for low-level bindings to the Gromacs trajectory file formats

## 5.13.1. Classes

class `MDAnalysis.coordinates.xdrfile.XTC.``Timestep`(arg)

  Timestep for a Gromacs XTC trajectory.

  `copy`()

    Make an independent (“deep”) copy of the whole `Timestep`.

  `dimensions`

    unitcell dimensions (A, B, C, alpha, beta, gamma)

    - A, B, C are the lengths of the primitive cell vectors e1, e2, e3
    - alpha = angle(e1, e2)
    - beta = angle(e1, e3)
    - gamma = angle(e2, e3)
  `volume`

    volume of the unitcell

class `MDAnalysis.coordinates.xdrfile.XTC.``XTCReader`(filename, convert_units=None, **kwargs)

  Read Gromacs XTC trajectory.

  `OtherWriter`(filename, **kwargs)

    Returns a writer appropriate for filename.

    Sets the default keywords start, step and delta (if available). numatoms is always set from `Reader.numatoms`.

    See also

    `Reader.Writer()` and `MDAnalysis.Writer()`

  `Writer`(filename, **kwargs)

    Returns a Gromacs TrjWriter for filename with the same parameters as this trajectory.

    All values can be changed through keyword arguments.

    Arguments : | filename filename of the output trajectory
    Keywords : | numatoms number of atoms delta Time interval between frames in ps. precision accuracy for lossy XTC format as a power of 10 (ignored for TRR) [1000.0]
    Returns : | appropriate `TrjWriter`

  `close`()

    Close xdr trajectory file if it was open.

  `close_trajectory`()

    Specific implementation of trajectory closing.

  `convert_forces_from_native`(force, inplace=True)

    In-place conversion of forces array force from native units to base units.

    By default, the input force is modified in place and also returned.

    New in version 0.7.7.

  `convert_forces_to_native`(force, inplace=True)

    In-place conversion of force array force from base units to native units.

    By default, the input force is modified in place and also returned.

    New in version 0.7.7.

  `convert_pos_from_native`(x, inplace=True)

    In-place conversion of coordinate array x from native units to base units.

    By default, the input x is modified in place and also returned.

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_pos_to_native`(x, inplace=True)

    Conversion of coordinate array x from base units to native units.

    By default, the input x is modified in place and also returned.

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_time_from_native`(t, inplace=True)

    Convert time t from native units to base units.

    By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_time_to_native`(t, inplace=True)

    Convert time t from base units to native units.

    By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_velocities_from_native`(v, inplace=True)

    In-place conversion of velocities array v from native units to base units.

    By default, the input v is modified in place and also returned.

    New in version 0.7.5.

  `convert_velocities_to_native`(v, inplace=True)

    In-place conversion of coordinate array v from base units to native units.

    By default, the input v is modified in place and also returned.

    New in version 0.7.5.

  `delta`

    Time step length in ps.

    The result is computed from the trajectory and cached. If for any reason the trajectory cannot be read then 0 is returned.

  `dt`

    Time between two trajectory frames in picoseconds.

  `frame`

    Frame number of the current time step.

    This is a simple short cut to `Timestep.frame`.

  `next`()

    Forward one step to next frame.

  `numatoms`

    Read the number of atoms from the trajectory.

    The result is cached. If for any reason the trajectory cannot be read then 0 is returned.

  `numframes`

    Read the number of frames from the trajectory.

    The result is cached. If for any reason the trajectory cannot be read then 0 is returned.

    This takes a long time because the frames are counted by iterating through the whole trajectory.

  `open_trajectory`()

    Open xdr trajectory file.

    Returns : | pointer to XDRFILE (and sets self.xdrfile)
    Raises : | `IOError` with code EALREADY if file was already opened or ENOENT if the file cannot be found

  `rewind`()

    Position at beginning of trajectory

  `time`

    Time of the current frame in MDAnalysis time units (typically ps).

    time = `Timestep.frame` * `Reader.dt`

  `totaltime`

    Total length of the trajectory numframes * dt.

class `MDAnalysis.coordinates.xdrfile.XTC.``XTCWriter`(filename, numatoms, start=0, step=1, delta=1.0, precision=1000.0, remarks=None, convert_units=None)

  Write a Gromacs XTC trajectory.

  Create a new TrjWriter

  Arguments : | filename name of output file numatoms number of atoms in trajectory file
  Keywords : | start starting timestep step skip between subsequent timesteps delta timestep precision accuracy for lossy XTC format [1000] convert_units `True`: units are converted to the MDAnalysis base format; `None` selects the value of `MDAnalysis.core.flags` [‘convert_gromacs_lengths’]. (see Flags)

  `close_trajectory`()

    Specific implementation of trajectory closing.

  `convert_dimensions_to_unitcell`(ts)

    Read dimensions from timestep ts and return Gromacs box vectors

  `convert_forces_from_native`(force, inplace=True)

    In-place conversion of forces array force from native units to base units.

    By default, the input force is modified in place and also returned.

    New in version 0.7.7.

  `convert_forces_to_native`(force, inplace=True)

    In-place conversion of force array force from base units to native units.

    By default, the input force is modified in place and also returned.

    New in version 0.7.7.

  `convert_pos_from_native`(x, inplace=True)

    In-place conversion of coordinate array x from native units to base units.

    By default, the input x is modified in place and also returned.

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_pos_to_native`(x, inplace=True)

    Conversion of coordinate array x from base units to native units.

    By default, the input x is modified in place and also returned.

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_time_from_native`(t, inplace=True)

    Convert time t from native units to base units.

    By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_time_to_native`(t, inplace=True)

    Convert time t from base units to native units.

    By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

    Changed in version 0.7.5: Keyword inplace can be set to `False` so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

  `convert_velocities_from_native`(v, inplace=True)

    In-place conversion of velocities array v from native units to base units.

    By default, the input v is modified in place and also returned.

    New in version 0.7.5.

  `convert_velocities_to_native`(v, inplace=True)

    In-place conversion of coordinate array v from base units to native units.

    By default, the input v is modified in place and also returned.

    New in version 0.7.5.

  `has_valid_coordinates`(criteria, x)

    Returns `True` if all values are within limit values of their formats.

    Due to rounding, the test is asymmetric (and min is supposed to be negative):

    > min < x <= max

    Arguments : | criteria dictionary containing the max and min values in native units x `numpy.ndarray` of `(x, y, z)` coordinates of atoms selected to be written out.
    Returns : | boolean

  `write`(obj)

    Write current timestep, using the supplied obj.

    The argument should be a `AtomGroup` or a `Universe` or a `Timestep` instance.

    Note

    The size of the obj must be the same as the number of atom provided when setting up the trajectory.

  `write_next_timestep`(ts=None)

    write a new timestep to the trj file

    ts is a `Timestep` instance containing coordinates to be written to trajectory file

class `MDAnalysis.coordinates.xdrfile.XTC.``Timestep`(arg)

  Timestep for a Gromacs XTC trajectory.

class `MDAnalysis.coordinates.xdrfile.XTC.``XTCReader`(filename, convert_units=None, **kwargs)

  Read Gromacs XTC trajectory.

class `MDAnalysis.coordinates.xdrfile.XTC.``XTCWriter`(filename, numatoms, start=0, step=1, delta=1.0, precision=1000.0, remarks=None, convert_units=None)

  Write a Gromacs XTC trajectory.

  Create a new TrjWriter

  Arguments : | filename name of output file numatoms number of atoms in trajectory file
  Keywords : | start starting timestep step skip between subsequent timesteps delta timestep precision accuracy for lossy XTC format [1000] convert_units `True`: units are converted to the MDAnalysis base format; `None` selects the value of `MDAnalysis.core.flags` [‘convert_gromacs_lengths’]. (see Flags)

### Navigation

- index
- modules |
- next |
- previous |
- MDAnalysis 0.7.7 documentation »
- 5. Coordinates modules »