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gmx-rotmat(1)			GROMACS Manual			 gmx-rotmat(1)

NAME
       gmx-rotmat - Plot the rotation matrix for fitting to a reference struc‐
       ture

SYNOPSIS
       gmx rotmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
		  [-n [<.ndx>]] [-o [<.xvg>]] [-nice <int>] [-b <time>]
		  [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
		  [-ref <enum>] [-skip <int>] [-[no]fitxy] [-[no]mw]

DESCRIPTION
       gmx rotmat plots the rotation matrix required for least squares fitting
       a conformation onto the reference conformation provided with -s. Trans‐
       lation 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	refer‐
       ence 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  gmx
       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.

OPTIONS
       Options to specify input and output files:

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

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

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

       -o [<.xvg>] (rotmat.xvg) (Output)
	   xvgr/xmgr file

       Other options:

       -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]w  (no)
	   View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
	   xvg plot formatting: xmgrace, xmgr, none

       -ref <enum> (none)
	   Determine the optimal reference structure: none, xyz, xy

       -skip <int> (1)
	   Use every nr-th frame for -ref

       -[no]fitxy  (no)
	   Fit the x/y rotation before determining the rotation

       -[no]mw	(yes)
	   Use mass weighted fitting

SEE ALSO
       gromacs(7)

       More   information  about  GROMACS  is  available  at  <http://www.gro‐
       macs.org/>.

VERSION 5.0.6							 gmx-rotmat(1)

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