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GMX-ROTMAT(1)			    GROMACS			 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/.gro/..._]] [-n [_.ndx_]]
		     [-o [_.xvg_]] [-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	refer-
       ence 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  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
       RMSDas  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 ma-
       trix.

OPTIONS
       Options to specify input	files:

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

       -s [<.tpr/.gro/^a|>] (topol.tpr)
	      Structure+mass(db): tpr gro g96 pdb brk ent

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

       Options to specify output files:

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

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit 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
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020			 GMX-ROTMAT(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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