gmx morph¶
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