gmx trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). 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 protein. 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.
With option -nshell the number of molecules within a shell of radius -r around the reference group are printed.
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
-o [<.xtc/.trr/...>] (ordered.xtc) (Output, Optional)
Trajectory: xtc trr trj gro g96 pdb tng
-nshell [<.xvg>] (nshell.xvg) (Output, Optional)
-nice <int> (19)
Set the nicelevel
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (ps)
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-na <int> (3)
Number of atoms in a molecule
-da <int> (1)
Atom used for the distance calculation, 0 is COM
Use the distance to the center of mass of the reference group
-r <real> (0)
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