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gmx-dyndom(1)			GROMACS Manual			 gmx-dyndom(1)

NAME
       gmx-dyndom - Interpolate and extrapolate structure rotations

SYNOPSIS
       gmx dyndom [-f [<.pdb>]] [-o [<.xtc/.trr/...>]] [-n [<.ndx>]]
		  [-nice <int>] [-firstangle <real>] [-lastangle <real>]
		  [-nframe <int>] [-maxangle <real>] [-trans <real>]
		  [-head <vector>] [-tail <vector>]

DESCRIPTION
       gmx    dyndom	reads	 a    .pdb    file    output	from	DynDom
       (http://www.cmp.uea.ac.uk/dyndom/). It reads the coordinates, the coor‐
       dinates of the rotation axis, and an index file containing the domains.
       Furthermore, it takes the first and last atom of the arrow file as com‐
       mand  line  arguments (head and tail) and finally it takes the transla‐
       tion vector (given in DynDom info file) and the angle of rotation (also
       as command line arguments). If the angle determined by DynDom is given,
       one should be able to recover the second structure used for  generating
       the DynDom output. Because of limited numerical accuracy this should be
       verified by computing an all-atom RMSD (using gmx confrms) rather  than
       by file comparison (using diff).

       The purpose of this program is to interpolate and extrapolate the rota‐
       tion as found by DynDom. As a result unphysical structures with long or
       short  bonds,  or overlapping atoms may be produced. Visual inspection,
       and energy minimization may be necessary to validate the structure.

OPTIONS
       Options to specify input and output files:

       -f [<.pdb>] (dyndom.pdb) (Input)
	   Protein data bank file

       -o [<.xtc/.trr/...>] (rotated.xtc) (Output)
	   Trajectory: xtc trr trj gro g96 pdb tng

       -n [<.ndx>] (domains.ndx) (Input)
	   Index file

       Other options:

       -nice <int> (0)
	   Set the nicelevel

       -firstangle <real> (0)
	   Angle of rotation about rotation vector

       -lastangle <real> (0)
	   Angle of rotation about rotation vector

       -nframe <int> (11)
	   Number of steps on the pathway

       -maxangle <real> (0)
	   DymDom dtermined angle of rotation about rotation vector

       -trans <real> (0)
	   Translation (Angstrom) along rotation vector (see DynDom info file)

       -head <vector> (0 0 0)
	   First atom of the arrow vector

       -tail <vector> (0 0 0)
	   Last atom of the arrow vector

SEE ALSO
       gromacs(7)

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

VERSION 5.0.6							 gmx-dyndom(1)

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