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.
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()
Reading of Gromacs TRR trajectories.
See also
MDAnalysis.coordinates.xdrfile.libxdrfile for low-level bindings to the Gromacs trajectory file formats
Timestep for a Gromacs TRR trajectory.
unitcell dimensions (A, B, C, alpha, beta, gamma)
volume of the unitcell
Read a Gromacs TRR trajectory.
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()
Returns a Gromacs TrjWriter for filename with the same parameters as this trajectory.
All values can be changed through keyword arguments.
Arguments : |
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Keywords : |
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Returns : | appropriate TrjWriter |
Close xdr trajectory file if it was open.
Specific implementation of trajectory closing.
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.
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 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 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.
In-place conversion of coordinate 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.
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.
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.
Time between two trajectory frames in picoseconds.
Frame number of the current time step.
This is a simple short cut to Timestep.frame.
Forward one step to next frame.
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.
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 xdr trajectory file.
Returns : | pointer to XDRFILE (and sets self.xdrfile) |
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Raises : | IOError with code EALREADY if file was already opened or ENOENT if the file cannot be found |
Position at beginning of trajectory
Time of the current frame in MDAnalysis time units (typically ps).
time = Timestep.frame * Reader.dt
Total length of the trajectory numframes * dt.
Write a Gromacs TRR trajectory.
Create a new TrjWriter
Arguments : |
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Keywords : |
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Specific implementation of trajectory closing.
Read dimensions from timestep ts and return Gromacs box vectors
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.
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 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 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.
In-place conversion of coordinate 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.
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.
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 : |
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Returns : | boolean |
Read a Gromacs TRR trajectory.
Write a Gromacs TRR trajectory.
Create a new TrjWriter
Arguments : |
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Keywords : |
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Timestep for a Gromacs TRR trajectory.