Man page - gmx-trjorder(1)
Packages contains this manual
- gmx-trjorder(1)
- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
- gmx-sham(1)
- gmx-helixorient(1)
- gmx-select(1)
- gmx-nmeig(1)
- gmx-density(1)
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- gmx-hydorder(1)
- gmx-editconf(1)
- gmx-msd(1)
- gmx-confrms(1)
- gmx-cluster(1)
- gmx-saltbr(1)
- gmx-potential(1)
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- gmx-make_ndx(1)
- gmx-enemat(1)
- gmx(1)
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- gmx-rotacf(1)
- gmx-helix(1)
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- gmx-pdb2gmx(1)
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- gmx-order(1)
- gmx-gangle(1)
- gmx-eneconv(1)
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- gmx-nonbonded-benchmark(1)
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- demux(1)
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- xplor2gmx(1)
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- gmx-rdf(1)
- gmx-pairdist(1)
- gmx-trjconv(1)
- gmx-traj(1)
- gmx_mpi_d(1)
- gmx-report-methods(1)
- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-TRJORDER
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-trjorder - Order molecules according to their distance to a group
SYNOPSIS
gmx trjorder
[
-f
[<.xtc/.trr/...>]
] [
-s
[<.tpr/.gro/...>]
] [
-n
[<.ndx>]
]
[
-o
[<.xtc/.trr/...>]
] [
-nshell
[<.xvg>]
] [
-b
<time>
]
[
-e
<time>
] [
-dt
<time>
] [
-xvg
<enum>
]
[
-na
<int>
]
[
-da
<int>
] [
-[no]com
] [
-r
<real>
] [
-[no]z
]
DESCRIPTION
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
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)
Index file
Options to
specify output files:
-o [<.xtc/.trr/...>] (ordered.xtc) (Optional)
Trajectory: xtc trr gro g96 pdb tng
-nshell [<.xvg>] (nshell.xvg) (Optional)
xvgr/xmgr file
Other options:
-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit 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
SEE ALSO
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
COPYRIGHT
2025, GROMACS development team