Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-morph - Interpolate linearly between conformations

SYNOPSIS

          gmx morph [-f1 [<.gro/.g96/...>]] [-f2 [<.gro/.g96/...>]] [-n [<.ndx>]]
                    [-o [<.xtc/.trr/...>]] [-or [<.xvg>]] [-[no]w]
                    [-xvg <enum>] [-ninterm <int>] [-first <real>]
                    [-last <real>] [-[no]fit]

DESCRIPTION

       gmx  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.

OPTIONS

       Options to specify input files:

       -f1 [<.gro/.g96/…>] (conf1.gro)
              Structure file: gro g96 pdb brk ent esp tpr

       -f2 [<.gro/.g96/…>] (conf2.gro)
              Structure file: gro g96 pdb brk ent esp tpr

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

       Options to specify output files:

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

       -or [<.xvg>] (rms-interm.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, 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]fit (yes)
              Do a least squares fit of the second to the first structure before interpolating

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2019, GROMACS development team