debian man page for g_rotmat

g_rotmat(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_rotmat(1)

NAME
       g_rotmat - plots the rotation matrix for fitting to a reference structure

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
       g_rotmat  -f  traj.xtc -s topol.tpr -n index.ndx -o rotmat.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ref
       enum -skip int -[no]fitxy -[no]mw

DESCRIPTION
	g_rotmat plots the rotation matrix required for least squares fitting a conformation onto the reference conformation provided  with    -s.
       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
       trjconv -fit rotxy+transxy to remove the rotation in the  x-y plane.

       Option	-ref  determines  a reference structure for fitting, instead of using the structure from  -s. 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
       -skip option can be useful. A full fit or only a fit in the  x-y plane can be performed.

       Option  -fitxy fits in the  x-y plane before determining the rotation matrix.

FILES
       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

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

       -n index.ndx Input, Opt.
	Index file

       -o rotmat.xvg Output
	xvgr/xmgr file

OTHER OPTIONS
       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -ref enum none
	Determine the optimal reference structure:  none,  xyz or  xy

       -skip int 1
	Use every nr-th frame for  -ref

       -[no]fitxyno
	Fit the x/y rotation before determining the rotation

       -[no]mwyes
	Use mass weighted fitting

SEE ALSO
       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_rotmat(1)