gmx morph

Main Table of Contents VERSION 5.0.7


gmx morph [-f1 [<.gro/.g96/...>]] [-f2 [<.gro/.g96/...>]]
          [-o [<.xtc/.trr/...>]] [-or [<.xvg>]] [-n [<.ndx>]] [-nice ]
          [-[no]w] [-xvg ] [-ninterm ] [-first ]
          [-last ] [-[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 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