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g_rotmatMain Table of Contents |
VERSION 4.6.5
Mon 2 Dec 2013
| VERSION 4.6.5 |
g_rotmat plots the rotation matrix required for least squares fitting a conformation onto the reference conformation provided with -s. Translation is removed before fitting. The output are the three vectors that give the new directions of the x, y and z directions of the reference conformation, for example: (zx,zy,zz) is the orientation of the reference z-axis in the trajectory frame.
This tool is useful for, for instance,
determining the orientation of a molecule
at an interface, possibly on a trajectory produced with
trjconv -fit rotxy+transxy to remove the rotation
in the
Option -ref determines a reference structure for fitting,
instead of using the structure from -s. The structure with
the lowest sum of RMSD's to all other structures is used.
Since the computational cost of this procedure grows with
the square of the number of frames, the -skip option
can be useful. A full fit or only a fit in the
Option -fitxy fits in the
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Trajectory: xtc trr trj gro g96 pdb cpt |
| -s | topol.tpr | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb |
| -n | index.ndx | Input, Opt. | Index file |
| -o | rotmat.xvg | Output | xvgr/xmgr file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -[no]version | bool | no | Print version info and quit |
| -nice | int | 19 | Set the nicelevel |
| -b | time | 0 | First frame (ps) to read from trajectory |
| -e | time | 0 | Last frame (ps) to read from trajectory |
| -dt | time | 0 | Only use frame when t MOD dt = first time (ps) |
| -[no]w | bool | no | View output .xvg, .xpm, .eps and .pdb files |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -ref | enum | none | Determine the optimal reference structure: none, xyz or xy |
| -skip | int | 1 | Use every nr-th frame for -ref |
| -[no]fitxy | bool | no | Fit the x/y rotation before determining the rotation |
| -[no]mw | bool | yes | Use mass weighted fitting |