Trajectory File

Trajectory files are files written initially by mdrun to contain atomic positions, velocities, and/or forces. The type of data and the period with which they are written are controlled with .mdp file options (see Analysing Trajectory Information). GROMACS will write full-precision portable-binary data in a format known as a .trr file and, optionally, a reduced-precision format for positions only, known as an .xtc file. The latter is useful when you know you will want positions for analysis with a higher frequency than the velocities, or only a subset of positions for analysis. The period (measured in integration steps) at which mdrun writes this output is given by the .mdp file options nstxout/nstvout/nstfout for the .trr file, and nstxtcout for the .xtc file.

You will need a full-precision frame with both positions and velocities in a .trr file (and maybe energies) for doing a restart, and GROMACS will always write one of these at the end of a run, regardless of the .mdp file options you chose.

The GROMACS analysis tools will read either format in all cases (that the author can think of!). Other analysis tools and visualization programs will vary, but in particular VMD will read both GROMACS trajectory formats.

Besides the .xtc and .trr formats, GROMACS can also print trajectories in .trj (full-precision), .g87, .g96, .gro, or .pdb (all of differing precision) formats.  Note that trajectories written in ASCII text consume much more disk space than those written in binary.

Recent versions of GROMACS can use VMD plugins to read non-native trajectory file formats.