g_morph(1) linear interpolation of conformations


g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -[no]version -nice int -[no]w -xvg enum -ninterm int -first real -last real -[no]fit


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 the group from which the RMS is computed.


-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 


 Print help info and quit

 Print version info and quit

-nice int 0
 Set the nicelevel

 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)

 Do a least squares fit of the second to the first structure before interpolating