.TH gmx-trjorder 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-trjorder \- Order molecules according to their distance to a group

.SH SYNOPSIS
gmx trjorder [\-f [<.xtc/.trr/...>]] [\-s [<.tpr/.tpb/...>]]
             [\-n [<.ndx>]] [\-o [<.xtc/.trr/...>]] [\-nshell [<.xvg>]]
             [\-nice <int>] [\-b <time>] [\-e <time>] [\-dt <time>]
             [\-xvg <enum>] [\-na <int>] [\-da <int>] [\-[no]com]
             [\-r <real>] [\-[no]z]

.SH DESCRIPTION
\fBgmx trjorder\fR orders molecules according to the smallest distance to atoms in a reference group or on z\-coordinate (with option \fB\-z\fR). 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 \fB\-da\fR 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 \fB\-da\fR to 0. All atoms in the trajectory are written to the output trajectory.

\fBgmx trjorder\fR 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 \fB.pdb\fR 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 \fB\-nshell\fR the number of molecules within a shell of radius \fB\-r\fR around the reference group are printed.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-o" " [<.xtc/.trr/...>] (ordered.xtc) (Output, Optional)"
    Trajectory: xtc trr trj gro g96 pdb tng

.BI "\-nshell" " [<.xvg>] (nshell.xvg) (Output, Optional)"
    xvgr/xmgr file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-na" " <int> (3)"
    Number of atoms in a molecule

.BI "\-da" " <int> (1)"
    Atom used for the distance calculation, 0 is COM

.BI "\-[no]com" "  (no)"
    Use the distance to the center of mass of the reference group

.BI "\-r" " <real> (0)"
    Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein

.BI "\-[no]z" "  (no)"
    Order molecules on z\-coordinate


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.