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gmx-morph(1)                    GROMACS Manual                    gmx-morph(1)

NAME
       gmx-morph - Interpolate linearly between conformations

SYNOPSIS
       gmx morph [-f1 [<.gro/.g96/...>]] [-f2 [<.gro/.g96/...>]]
                 [-o [<.xtc/.trr/...>]] [-or [<.xvg>]] [-n [<.ndx>]]
                 [-nice <int>] [-[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 and output files:

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

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

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

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

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

       Other options:

       -nice <int> (0)
           Set the nicelevel

       -[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
       gromacs(7)

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

VERSION 5.0.6                                                     gmx-morph(1)