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GMX-TRJORDER(1)			    GROMACS		       GMX-TRJORDER(1)

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 mole-
       cules 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.  Ras-
       mol.

       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/^a|>] (traj.xtc)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/^a|>] (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/^a|>] (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 num-
	      ber 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
       2020, GROMACS development team

2020.3				 Jul 09, 2020		       GMX-TRJORDER(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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