Provided by: gromacs-data_2019.3-2_all bug

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

       2019, GROMACS development team