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)