NAME

       trjorder - orders molecules according to their distance to a group

       VERSION 4.6.5

SYNOPSIS

       trjorder  -f  traj.xtc  -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h
       -[no]version -nice int -b time -e time -dt time -xvg enum -na int -da int -[no]com -r real
       -[no]z

DESCRIPTION

         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.

         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.

FILES

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -o ordered.xtc Output, Opt.
        Trajectory: xtc trr trj gro g96 pdb

       -nshell nshell.xvg Output, Opt.
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -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 or  none

       -na int 3
        Number of atoms in a molecule

       -da int 1
        Atom used for the distance calculation, 0 is COM

       -[no]comno
        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]zno
        Order molecules on z-coordinate

SEE ALSO

       gromacs(7)

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

                                          Mon 2 Dec 2013                              trjorder(1)