trjorder(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       trjorder(1)

NAME

       trjorder - orders molecules according to their distance to a group

       VERSION 4.5.4-dev-20110404-bc5695c

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 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.

	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 4 Apr 2011						       trjorder(1)