| 
 | VERSION 3.3.1 | 
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 strucutre 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.
| option | filename | type | description | 
|---|---|---|---|
| -f1 | conf1.gro | Input | Generic structure: gro g96 pdb tpr tpb tpa xml | 
| -f2 | conf2.gro | Input | Generic structure: gro g96 pdb tpr tpb tpa xml | 
| -o | interm.xtc | Output | Generic trajectory: xtc trr trj gro g96 pdb | 
| -or | rms-interm.xvg | Output, Opt. | xvgr/xmgr file | 
| -n | index.ndx | Input, Opt. | Index file | 
| option | type | default | description | 
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit | 
| -nice | int | 0 | Set the nicelevel | 
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files | 
| -[no]xvgr | bool | yes | Add specific codes (legends etc.) in the output xvg files for the xmgrace program | 
| -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 | bool | yes | Do a least squares fit of the second to the first structure before interpolating |