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g_morphMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
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.
| option | filename | type | description |
|---|---|---|---|
| -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 |
| option | type | default | description |
|---|---|---|---|
| -[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 |