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g_rmsdistMain Table of Contents |
VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty
Thu 26 Aug 2010
| VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty |
g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed by g_rms. The reference structure is taken from the structure file. The rmsd at time t is calculated as the rms of the differences in distance between atom-pairs in the reference structure and the structure at time t.
g_rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists of atom pairs with 1/r^3 and 1/r^6 averaged distance below the maximum distance (-max, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named *[123]). Additionally a list of equivalent atoms can be supplied (-equiv), each line containing a set of equivalent atoms specified as residue number and name and atom name; e.g.:
3 SER HB1 3 SER HB2
Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined.
| 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 |
| -equiv | equiv.dat | Input, Opt. | Generic data file |
| -o | distrmsd.xvg | Output | xvgr/xmgr file |
| -rms | rmsdist.xpm | Output, Opt. | X PixMap compatible matrix file |
| -scl | rmsscale.xpm | Output, Opt. | X PixMap compatible matrix file |
| -mean | rmsmean.xpm | Output, Opt. | X PixMap compatible matrix file |
| -nmr3 | nmr3.xpm | Output, Opt. | X PixMap compatible matrix file |
| -nmr6 | nmr6.xpm | Output, Opt. | X PixMap compatible matrix file |
| -noe | noe.dat | Output, Opt. | Generic data 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 | 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 | gmx_bool | no | View output xvg, xpm, eps and pdb files |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -nlevels | int | 40 | Discretize rms in # levels |
| -max | real | -1 | Maximum level in matrices |
| -[no]sumh | gmx_bool | yes | average distance over equivalent hydrogens |
| -[no]pbc | gmx_bool | yes | Use periodic boundary conditions when computing distances |