.TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
trjorder - orders molecules according to their distance to a group

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3trjorder\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " ordered.xtc "
.BI "\-nshell" " nshell.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-xvg" " enum "
.BI "\-na" " int "
.BI "\-da" " int "
.BI "\-[no]com" ""
.BI "\-r" " real "
.BI "\-[no]z" ""
.SH DESCRIPTION
\&\fB 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.


\&\fB 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 FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " ordered.xtc" 
.B Output, Opt.
 Trajectory: xtc trr trj gro g96 pdb 

.BI "\-nshell" " nshell.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.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: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.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>.