gmx trjconv [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-fr [<.ndx>]] [-sub [<.ndx>]] [-drop [<.xvg>]] [-o [<.xtc/.trr/...>]] [-b <time>] [-e <time>] [-tu <enum>] [-[no]w] [-xvg <enum>] [-skip <int>] [-dt <time>] [-[no]round] [-dump <time>] [-t0 <time>] [-timestep <time>] [-pbc <enum>] [-ur <enum>] [-[no]center] [-boxcenter <enum>] [-box <vector>] [-trans <vector>] [-shift <vector>] [-fit <enum>] [-ndec <int>] [-[no]vel] [-[no]force] [-trunc <time>] [-exec <string>] [-split <time>] [-[no]sep] [-nzero <int>] [-dropunder <real>] [-dropover <real>] [-[no]conect]
gmx trjconv can convert trajectory files in many ways:
from one format to another
select a subset of atoms
change the periodicity representation
keep multimeric molecules together
center atoms in the box
fit atoms to reference structure
reduce the number of frames
change the timestamps of the frames (
select frames within a certain range of a quantity given in an .xvg file.
The option to write subtrajectories (-sub) based on the information obtained from
cluster analysis has been removed from
gmx trjconv and is now part of
gmx trjcat is better suited for concatenating multiple trajectory files.
The following formats are supported for input and output:
.xtc, .trr, .gro,
.pdb and .tng.
The file formats are detected from the file extension.
The precision of the .xtc output is taken from the
input file for .xtc, .gro and .pdb,
and from the
-ndec option for other input formats. The precision
is always taken from
-ndec, when this option is set.
All other formats have fixed precision. .trr
output can be single or double precision, depending on the precision
gmx trjconv binary.
Note that velocities are only supported in
.trr, .tng, .gro and
-sep can be used to write every frame to a separate
.gro, .g96 or .pdb file. By default, all frames all written to
.pdb files with all frames concatenated can be viewed with
It is possible to select part of your trajectory and write it out to a new trajectory file in order to save disk space, e.g. for leaving out the water from a trajectory of a protein in water. ALWAYS put the original trajectory on tape! We recommend to use the portable .xtc format for your analysis to save disk space and to have portable files. When writing .tng output the file will contain one molecule type of the correct count if the selection name matches the molecule name and the selected atoms match all atoms of that molecule. Otherwise the whole selection will be treated as one single molecule containing all the selected atoms.
There are two options for fitting the trajectory to a reference either for essential dynamics analysis, etc. The first option is just plain fitting to a reference structure in the structure file. The second option is a progressive fit in which the first timeframe is fitted to the reference structure in the structure file to obtain and each subsequent timeframe is fitted to the previously fitted structure. This way a continuous trajectory is generated, which might not be the case when using the regular fit method, e.g. when your protein undergoes large conformational transitions.
-pbc sets the type of periodic boundary condition
molputs the center of mass of molecules in the box, and requires a run input file to be supplied with
resputs the center of mass of residues in the box.
atomputs all the atoms in the box.
nojumpchecks if atoms jump across the box and then puts them back. This has the effect that all molecules will remain whole (provided they were whole in the initial conformation). Note that this ensures a continuous trajectory but molecules may diffuse out of the box. The starting configuration for this procedure is taken from the structure file, if one is supplied, otherwise it is the first frame.
clusterclusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster, which is iteratively updated. Note that this will only give meaningful results if you in fact have a cluster. Luckily that can be checked afterwards using a trajectory viewer. Note also that if your molecules are broken this will not work either.
wholeonly makes broken molecules whole.
-ur sets the unit cell representation for options
All three options give different results for triclinic boxes and
identical results for rectangular boxes.
rect is the ordinary brick shape.
tric is the triclinic unit cell.
compact puts all atoms at the closest distance from the center
of the box. This can be useful for visualizing e.g. truncated octahedra
or rhombic dodecahedra. The center for options
tric (see below), unless the option
is set differently.
-center centers the system in the box. The user can
select the group which is used to determine the geometrical center.
-boxcenter sets the location of the center of the box
-center. The center options are:
tric: half of the sum of the box vectors,
rect: half of the box diagonal,
-pbc mol in addition to
-center when you
want all molecules in the box after the centering.
-box sets the size of the new box. This option only works
for leading dimensions and is thus generally only useful for rectangular boxes.
If you want to modify only some of the dimensions, e.g. when reading from
a trajectory, you can use -1 for those dimensions that should stay the same
It is not always possible to use combinations of
-center to do exactly what
you want in one call to
gmx trjconv. Consider using multiple
calls, and check out the GROMACS website for suggestions.
-dt, it is possible to reduce the number of
frames in the output. This option relies on the accuracy of the times
in your input trajectory, so if these are inaccurate use the
-timestep option to modify the time (this can be done
simultaneously). For making smooth movies, the program gmx filter
can reduce the number of frames while using low-pass frequency
filtering, this reduces aliasing of high frequency motions.
gmx trjconv can truncate .trr in place, i.e.
without copying the file. This is useful when a run has crashed
during disk I/O (i.e. full disk), or when two contiguous
trajectories must be concatenated without having double frames.
-dump can be used to extract a frame at or near
one specific time from your trajectory. If the frames in the trajectory are
not in temporal order, the result is unspecified.
-drop reads an .xvg file with times and values.
-dropover are set,
frames with a value below and above the value of the respective options
will not be written.
Options to specify input files:
-s[<.tpr/.gro/…>] (topol.tpr) (Optional)
-n[<.ndx>] (index.ndx) (Optional)
-fr[<.ndx>] (frames.ndx) (Optional)
-sub[<.ndx>] (cluster.ndx) (Optional)
-drop[<.xvg>] (drop.xvg) (Optional)
Options to specify output files:
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Unit for time values: fs, ps, ns, us, ms, s
xvg plot formatting: xmgrace, xmgr, none
Only write every nr-th frame
Only write frame when t MOD dt = first time (ps)
Round measurements to nearest picosecond
Dump frame nearest specified time (ps)
Starting time (ps) (default: don’t change)
Change time step between input frames (ps)
PBC treatment (see help text for full description): none, mol, res, atom, nojump, cluster, whole
Unit-cell representation: rect, tric, compact
Center atoms in box
Center for -pbc and -center: tric, rect, zero
-box<vector> (0 0 0)
Size for new cubic box (default: read from input)
-trans<vector> (0 0 0)
All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact.
-shift<vector> (0 0 0)
All coordinates will be shifted by framenr*shift
Fit molecule to ref structure in the structure file: none, rot+trans, rotxy+transxy, translation, transxy, progressive
Number of decimal places to write to .xtc output
Read and write velocities if possible
Read and write forces if possible
Truncate input trajectory file after this time (ps)
Execute command for every output frame with the frame number as argument
Start writing new file when t MOD split = first time (ps)
Write each frame to a separate .gro, .g96 or .pdb file
If the -sep flag is set, use these many digits for the file numbers and prepend zeros as needed
Drop all frames below this value
Drop all frames above this value
Add CONECT PDB records when writing .pdb files. Useful for visualization of non-standard molecules, e.g. coarse grained ones