gmx trjorder¶
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