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       g_morph - linear interpolation of conformations

       VERSION 4.0.1


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


       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 strucutre 2.  If you specify first  0 or last  1 extrapolation
       will be on the path from input structure  x1  to  x2.  In  general  the
       coordinates  of  the  intermediate  x(i)  out  of  N total intermidates
       correspond to:

       x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)

       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 what group RMS is computed from.


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

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

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

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

       -n index.ndx Input, Opt.
        Index file


        Print help info and quit

       -nice int 0
        Set the nicelevel

        View output xvg, xpm, eps and pdb files

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -ninterm int 11
        Number of intermediates

       -first real 0
        Corresponds to first generated structure (0 is input x0, see above)

       -last real 1
        Corresponds to last generated structure (1 is input x1, see above)

        Do  a  least  squares  fit of the second to the first structure before



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                                Thu 16 Oct 2008                     g_morph(1)