NAME
trjorder - orders molecules according to their distance to a group
VERSION 4.0.1
SYNOPSIS
trjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell
nshell.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -na int
-da int -[no]com -r real
DESCRIPTION
trjorder orders molecules according to the smallest distance to atoms
in a reference group. 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. 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 refernce 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
-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)
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-na int 3
Number of atoms in a molecule
-da int 1
Atom used for the distance calculation
-[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
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 trjorder(1)