| VERSION 3.1 |
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 | Generic trajectory: xtc trr trj gro g96 pdb |
-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 |