Main Table of Contents

Thu 26 Aug 2010


g_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 x1 to x2. In general the coordinates of the intermediate x(i) out of N total intermidates correspond to:

x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)

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 what group RMS is computed from.


-f1 conf1.gro Input Structure file: gro g96 pdb tpr etc.
-f2 conf2.gro Input Structure file: gro g96 pdb tpr etc.
-o interm.xtc Output Trajectory: xtc trr trj gro g96 pdb cpt
-or rms-interm.xvg Output, Opt. xvgr/xmgr file
-n index.ndx Input, Opt. Index file

Other options

-[no]h gmx_bool no Print help info and quit
-[no]version gmx_bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]w gmx_bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-ninterm int 11 Number of intermediates
-first real 0 Corresponds to first generated structure (0 is input x0, see above)
-last real 1 Corresponds to last generated structure (1 is input x1, see above)
-[no]fit gmx_bool yes Do a least squares fit of the second to the first structure before interpolating