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)