gmx-trjorder man page
gmx-trjorder — Order molecules according to their distance to a group
gmx 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 molecules 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.
gmx 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.
Options to specify input files:
- -f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
- -s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
- -n [<.ndx>] (index.ndx) (Optional)
Options to specify output files:
- -o [<.xtc/.trr/...>] (ordered.xtc) (Optional)
Trajectory: xtc trr gro g96 pdb tng
- -nshell [<.xvg>] (nshell.xvg) (Optional)
- -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, none
- -na <int> (3)
Number of atoms in a molecule
- -da <int> (1)
Atom used for the distance calculation, 0 is COM
- -[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
- -[no]z (no)
Order molecules on z-coordinate
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2017, GROMACS development team