trjorder(1)
NAME
trjorder - orders molecules according to their distance to a group
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.
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -n index.ndx Input, Opt.
- Index file
- -o ordered.xtc Output
- Generic trajectory: xtc trr trj gro g96 pdb
- -nshell nshell.xvg Output, Opt.
- xvgr/xmgr file
OTHER OPTIONS
- -[no]h no
- 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]xvgr yes
- 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]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 number of
- molecules in a shell around e.g. a protein
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.