.TH g_rotmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rotmat - plots the rotation matrix for fitting to a reference structure

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rotmat\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " rotmat.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-ref" " enum "
.BI "\-skip" " int "
.BI "\-[no]fitxy" ""
.BI "\-[no]mw" ""
.SH DESCRIPTION
\&\fB g_rotmat\fR plots the rotation matrix required for least squares fitting
\&a conformation onto the reference conformation provided with
\&\fB \-s\fR. Translation is removed before fitting.
\&The output are the three vectors that give the new directions
\&of the x, y and z directions of the reference conformation,
\&for example: (zx,zy,zz) is the orientation of the reference
\&z\-axis in the trajectory frame.
\&


\&This tool is useful for, for instance,
\&determining the orientation of a molecule
\&at an interface, possibly on a trajectory produced with
\&\fB trjconv \-fit rotxy+transxy\fR to remove the rotation
\&in the \fI x\-y\fR plane.
\&


\&Option \fB \-ref\fR determines a reference structure for fitting,
\&instead of using the structure from \fB \-s\fR. The structure with
\&the lowest sum of RMSD's to all other structures is used.
\&Since the computational cost of this procedure grows with
\&the square of the number of frames, the \fB \-skip\fR option
\&can be useful. A full fit or only a fit in the \fI x\-y\fR plane can
\&be performed.
\&


\&Option \fB \-fitxy\fR fits in the \fI x\-y\fR plane before determining
\&the rotation matrix.
.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" " rotmat.xvg" 
.B Output
 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 "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-ref"  " enum" " none" 
 Determine the optimal reference structure: \fB none\fR, \fB xyz\fR or \fB xy\fR

.BI "\-skip"  " int" " 1" 
 Use every nr\-th frame for \fB \-ref\fR

.BI "\-[no]fitxy"  "no    "
 Fit the x/y rotation before determining the rotation

.BI "\-[no]mw"  "yes   "
 Use mass weighted fitting

.SH SEE ALSO
.BR gromacs(7)

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