NAME

       gmx-trjorder - Order molecules according to their distance to a group

SYNOPSIS

          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]

DESCRIPTION

       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

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xtc/.trr/...>] (ordered.xtc) (Optional)
              Trajectory: xtc trr gro g96 pdb tng

       -nshell [<.xvg>] (nshell.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit 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

       -[no]com (no)
              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

       -[no]z (no)
              Order molecules on z-coordinate

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-TRJORDER(1)