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GMX-MORPH(1) GROMACS GMX-MORPH(1)

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:

Structure file: gro g96 pdb brk ent esp tpr
Structure file: gro g96 pdb brk ent esp tpr
Index file

Options to specify output files:

Trajectory: xtc trr cpt gro g96 pdb tng
xvgr/xmgr file

Other options:

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr, none
Number of intermediates
Corresponds to first generated structure (0 is input x_1, see above)
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)

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2019, GROMACS development team

February 15, 2019 2019.1