gmx trjorder [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-nshell [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>] [-na <int>] [-da <int>] [-[no]com] [-r <real>] [-[no]z]
gmx trjorder orders molecules according to the smallest distance
to atoms in a reference group
or on z-coordinate (with option
With distance ordering, it will ask for a group of reference
atoms and a group of molecules. For each frame of the trajectory
the selected molecules will be reordered according to the shortest
distance between atom number
-da in the molecule and all the
atoms in the reference group. The center of mass of the molecules can
be used instead of a reference atom by setting
-da to 0.
All atoms in the trajectory are written
to the output trajectory.
gmx trjorder can be useful for e.g. analyzing the n waters closest to a
In that case the reference group would be the protein and the group
of molecules would consist of all the water atoms. When an index group
of the first n waters is made, the ordered trajectory can be used
with any GROMACS program to analyze the n closest waters.
If the output file is a .pdb file, the distance to the reference target will be stored in the B-factor field in order to color with e.g. Rasmol.
-nshell the number of molecules within a shell
-r around the reference group are printed.
Options to specify input files:
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
-o[<.xtc/.trr/…>] (ordered.xtc) (Optional)
-nshell[<.xvg>] (nshell.xvg) (Optional)
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
Number of atoms in a molecule
Atom used for the distance calculation, 0 is COM
Use the distance to the center of mass of the reference group
Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
Order molecules on z-coordinate