NAME

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

       VERSION 4.6.5

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 2 Dec 2013                                      g_rotmat(1)