Provided by: gromacs-data_2018.1-1_all
gmx-morph - Interpolate linearly between conformations
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]
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 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
gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>.
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