trjorder

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