NAME

       g_morph - linear interpolation of conformations VERSION 4.6.5

SYNOPSIS

       g_morph  -f1  conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h
       -[no]version -nice int -[no]w -xvg enum -ninterm int -first real -last real -[no]fit

DESCRIPTION

        g_morph does a linear interpolation of conformations in order to create intermediates. Of
       course  these  are completely unphysical, but that you may try to justify yourself. Output
       is in the form of a generic trajectory. The number of intermediates can be controlled with
       the   -ninterm  flag.  The  first  and last flag correspond to the way of interpolating: 0
       corresponds to input structure 1 while 1 corresponds to input structure 2.  If you specify
       -first   0 or  -last  1 extrapolation will be on the path from input structure x_1 to x_2.
       In general, the coordinates  of  the  intermediate  x(i)  out  of  N  total  intermediates
       correspond to:

       x(i) = x_1 + (first+(i/(N-1))*(last-first))*(x_2-x_1)

       Finally  the  RMSD  with  respect  to  both input structures can be computed if explicitly
       selected ( -or option). In that case, an index file may be read to select the  group  from
       which the RMS is computed.

FILES

       -f1 conf1.gro Input
        Structure file: gro g96 pdb tpr etc.

       -f2 conf2.gro Input
        Structure file: gro g96 pdb tpr etc.

       -o interm.xtc Output
        Trajectory: xtc trr trj gro g96 pdb cpt

       -or rms-interm.xvg Output, Opt.
        xvgr/xmgr file

       -n index.ndx Input, Opt.
        Index file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 0
        Set the nicelevel

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -ninterm int 11
        Number of intermediates

       -first real 0
        Corresponds to first generated structure (0 is input x_1, see above)

       -last real 1
        Corresponds to last generated structure (1 is input x_2, see above)

       -[no]fityes
        Do a least squares fit of the second to the first structure before interpolating

SEE ALSO

       gromacs(7)

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

                                          Mon 2 Dec 2013                               g_morph(1)