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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
       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 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.gromacs.org/>.

VERSION 5.0.6                                                    gmx-dyndom(1)