5.18. Gromacs portable run input TPR format parser

The TPRParser module allows reading of a Gromacs portable run input file (a TPR file). Because the file format of the TPR file is changing rapidly, not all versions are currently supported. The known working versions and the approximate Gromacs release numbers are listed in the table TPR format versions.

TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().
TPX format TPX generation Gromacs release read
?? ?? 3.3, 3.3.1 no
58 17 4.0, 4.0.2, 4.0.3, 4.0.4, 4.0.5, 4.0.6, 4.0.7 yes
73 23 4.5.0, 4.5.1, 4.5.2, 4.5.3, 4.5.4, 4.5.5 yes
83 24 4.6, 4.6.1 yes
100 26 5.0, 5.0.1, 5.0.2, 5.0.3,5.0.4, 5.0.5 yes
103 26 5.1 yes
110 26 2016 yes
112 26 2018 yes

For further discussion and notes see Issue 2. Please open a new issue in the Issue Tracker when a new or different TPR file format version should be supported.

Bonded interactions available in Gromacs are described in table 5.5 of the Gromacs manual. The following ones are used to build the topology (see Issue 463):

  • bonds: regular bonds (type 1), G96 bonds (type 2), Morse (type 3), cubic bonds (type 4), connections (type 5), harmonic potentials (type 6), FENE bonds (type 7), restraint potentials (type 10), tabulated potential with exclusion/connection (type 8), tabulated potential without exclusion/connection (type 9), constraints with exclusion/connection (type 1), constraints without exclusion/connection (type 2), SETTLE constraints
  • angles: regular angles (type 1), G96 angles (type 2), cross bond-bond (type3), cross-bond-angle (type 4), Urey-Bradley (type 5), quartic angles (type 6), restricted bending potential (type 10), tabulated angles (type 8)
  • dihedrals: proper dihedrals (type 1 and type 9), Ryckaert-Bellemans dihedrals (type 3), Fourier dihedrals (type 5), restricted dihedrals (type 10), combined bending-torsion potentials (type 11), tabulated dihedral (type 8)
  • impropers: improper dihedrals (type 2), periodic improper dihedrals (type 4)

5.18.1. Classes

class MDAnalysis.topology.TPRParser.TPRParser(filename)[source]

Read topology information from a Gromacs TPR file.

close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

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

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

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.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

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.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

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.) In-place operations improve performance because allocating new arrays is avoided.

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.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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)

Conversion of velocities array v from native to base units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

parse(**kwargs)[source]

Parse a Gromacs TPR file into a MDAnalysis internal topology structure.

Returns:structure
Return type:dict

5.18.2. Development notes

The TPR reader is a pure-python implementation of a basic TPR parser. Currently the following sections of the topology are parsed:

  • Atoms: number, name, type, resname, resid, segid, mass, charge, [residue, segment, radius, bfactor, resnum, moltype]
  • Bonds
  • Angels
  • Dihedrals
  • Impropers

This tpr parser is written according to the following files

  • gromacs_dir/src/kernel/gmxdump.c
  • gromacs_dir/src/gmxlib/tpxio.c (the most important one)
  • gromacs_dir/src/gmxlib/gmxfio_rw.c
  • gromacs_dir/src/gmxlib/gmxfio_xdr.c
  • gromacs_dir/include/gmxfiofio.h

or their equivalent in more recent versions of Gromacs.

The function read_tpxheader() is based on the TPRReaderDevelopment notes. Functions with names starting with read_ or do_ are trying to be similar to those in gmxdump.c or tpxio.c, those with extract_ are new.

Wherever fver_err(fver) is used, it means the tpx version problem has not been solved. Versions prior to Gromacs 4.0.x are not supported.