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5.13. Gromacs TRR file IO — MDAnalysis.coordinates.TRR

The Gromacs TRR trajectory format is a lossless format like e.g. the DCD format (see DCD) and unlike the XTC format, which stores reduced precision coordinates. Therefore, if one wants to convert to Gromacs trajectories without loss of precision then one should use the TRR format.

The TRR format can store velocities and forces in addition to coordinates. It is also used by other Gromacs tools to store and process other data such as modes from a principal component analysis.

5.13.1. Tips and Tricks

5.13.1.1. Filling a TRR with PCA modes

The following recipe by Ramon Crehuet shows how to convert modes stored in a NumPy-like array (e.g. from a PCA analysis with MMTK) to a TRR usable by Gromacs. The idea is to manually fill a Timestep with the desired values and then write it to a file with the appropriate TRRWriter. In order to respect the Gromacs format for modes in a TRR file, one must write the average coordinates in the first frame of the TRR and the modes into subsequent ones. The mode number is stored in the step attribute and the mode coordinates are filling the _pos attribute of Timestep:

# 'modes' is a mode object with M PCs, similar to a MxNx3 array
# 'xav' the average coordinates, a Nx3 array for N atoms

N = len(xav)   # number of atoms, i.e. number of coordinates

W = Writer('pca.trr', numatoms=N)            # TRR writer
ts = MDAnalysis.coordinates.TRR.Timestep(N)  # TRR time step

for frame,mode in enumerate(modes[4:16]):
    ts.lmbda = -1
    if frame<=1:
       ts._pos[:] = xav
    else:
       ts._pos[:] = mode.scaledToNorm(1.).array*10   # nm to angstroms
    ts.frame = frame         # manually change the frame number
    ts.step = frame - 1
    if frame <= 1:
       ts.time = frame-1
    else:
       ts.time = mode.frequency
    W.write(ts)             # converts angstrom to nm for gmx

 W.close()

5.13.2. Module reference

Reading of Gromacs TRR trajectories.

See also

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

5.13.2.1. Classes

class MDAnalysis.coordinates.xdrfile.TRR.Timestep(arg)[source]

Timestep for a Gromacs TRR 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.TRR.TRRReader(filename, convert_units=None, sub=None, **kwargs)[source]

Read a Gromacs TRR trajectory.

Arguments:
filename
the name of the trr file.

sub

an numpy integer array of what subset of trajectory atoms to load into the timestep. Intended to work similarly to the ‘sub’ argument to gromac’s trjconv.

This is usefull when one has a Universe loaded with only an unsolvated protein, and wants to read a solvated trajectory.

The length of this array must be <= to the actual number of atoms in the trajectory, and equal to number of atoms in the Universe.

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.

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.

load_offsets(filename)

Loads current trajectory offsets from filename (numpy format).

next()

Forward one step to next frame.

numatoms

The number of publically available atoms that this reader will store in the timestep.

If ‘sub’ was not given in the ctor, then this value will just be the actual number of atoms in the underlying trajectory file. If however ‘sub’ was given, then this value is the number specified by the ‘sub’ sub-selection.

If for any reason the trajectory cannot be read then a negative value 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

save_offsets(filename)

Saves current trajectory offsets into filename (numpy format).

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.TRR.TRRWriter(filename, numatoms, start=0, step=1, delta=None, precision=1000.0, remarks=None, convert_units=None)[source]

Write a Gromacs TRR trajectory.

Create a new TrjWriter

Arguments:
filename

name of output file

numatoms

number of atoms in trajectory file

Keywords:
start

starting timestep; only used when delta is set.

step

skip between subsequent timesteps; only used when delta is set.

delta

timestep to use. If set will override any time information contained in the passed Timestep objects; otherwise that will be used. If in the latter case Timestep.time is unavailable the TrjWriter will default to setting the trajectory time at 1 MDAnalysis unit (typically 1ps) per step.

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.TRR.TRRReader(filename, convert_units=None, sub=None, **kwargs)[source]

Read a Gromacs TRR trajectory.

Arguments:
filename
the name of the trr file.

sub

an numpy integer array of what subset of trajectory atoms to load into the timestep. Intended to work similarly to the ‘sub’ argument to gromac’s trjconv.

This is usefull when one has a Universe loaded with only an unsolvated protein, and wants to read a solvated trajectory.

The length of this array must be <= to the actual number of atoms in the trajectory, and equal to number of atoms in the Universe.

class MDAnalysis.coordinates.xdrfile.TRR.TRRWriter(filename, numatoms, start=0, step=1, delta=None, precision=1000.0, remarks=None, convert_units=None)[source]

Write a Gromacs TRR trajectory.

Create a new TrjWriter

Arguments:
filename

name of output file

numatoms

number of atoms in trajectory file

Keywords:
start

starting timestep; only used when delta is set.

step

skip between subsequent timesteps; only used when delta is set.

delta

timestep to use. If set will override any time information contained in the passed Timestep objects; otherwise that will be used. If in the latter case Timestep.time is unavailable the TrjWriter will default to setting the trajectory time at 1 MDAnalysis unit (typically 1ps) per step.

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)

class MDAnalysis.coordinates.xdrfile.TRR.Timestep(arg)[source]

Timestep for a Gromacs TRR trajectory.