gmx-morph1
Interpolate linearly between conformations
Usage
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]
Overview
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 |
Releases
3 releases since Debian 8 (Jessie); the text changed 2 times.