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.
