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NAME

       gmx-dyndom - Interpolate and extrapolate structure rotations

SYNOPSIS

          gmx dyndom [-f [<.pdb>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]]
                     [-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 coordinates of the rotation axis, and an index file  containing
       the  domains.   Furthermore, it takes the first and last atom of the arrow file as command
       line arguments (head and tail) and finally it  takes  the  translation  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 rotation 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 files:

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

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

       Options to specify output files:

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

       Other options:

       -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

       gmx(1)

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

COPYRIGHT

       2019, GROMACS development team