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g_rmsMain Table of Contents |
VERSION 3.2.0
Sun 25 Jan 2004
| VERSION 3.2.0 |
g_rms compares two structures by computing the root mean square deviation (RMSD), the size-independent 'rho' similarity parameter (rho) or the scaled rho (rhosc), see Maiorov & Crippen, PROTEINS 22, 273 (1995). This is selected by -what.
Each structure from a trajectory (-f) is compared to a reference structure. The reference structure is taken from the structure file (-s).
With option -mir also a comparison with the mirror image of the reference structure is calculated. This is useful as a reference for 'significant' values, see Maiorov & Crippen, PROTEINS 22, 273 (1995).
Option -prev produces the comparison with a previous frame the specified number of frames ago.
Option -m produces a matrix in .xpm format of comparison values of each structure in the trajectory with respect to each other structure. This file can be visualized with for instance xv and can be converted to postscript with xpm2ps.
Option -fit controls the least-squares fitting of the structures on top of each other: complete fit (rotation and translation), translation only, or no fitting at all.
With -f2, the 'other structures' are taken from a second trajectory, this generates a comparison matrix of one trajectory versus the other.
Option -bin does a binary dump of the comparison matrix.
Option -bm produces a matrix of average bond angle deviations analogously to the -m option. Only bonds between atoms in the comparison group are considered.
| option | filename | type | description |
|---|---|---|---|
| -s | topol.tpr | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb xml |
| -f | traj.xtc | Input | Generic trajectory: xtc trr trj gro g96 pdb |
| -f2 | traj.xtc | Input, Opt. | Generic trajectory: xtc trr trj gro g96 pdb |
| -n | index.ndx | Input, Opt. | Index file |
| -o | rmsd.xvg | Output | xvgr/xmgr file |
| -mir | rmsdmir.xvg | Output, Opt. | xvgr/xmgr file |
| -a | avgrp.xvg | Output, Opt. | xvgr/xmgr file |
| -dist | rmsd-dist.xvg | Output, Opt. | xvgr/xmgr file |
| -m | rmsd.xpm | Output, Opt. | X PixMap compatible matrix file |
| -bin | rmsd.dat | Output, Opt. | Generic data file |
| -bm | bond.xpm | Output, Opt. | X PixMap compatible matrix file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -nice | int | 19 | Set the nicelevel |
| -b | time | -1 | First frame (ps) to read from trajectory |
| -e | time | -1 | Last frame (ps) to read from trajectory |
| -dt | time | -1 | Only use frame when t MOD dt = first time (ps) |
| -tu | enum | ps | Time unit: ps, fs, ns, us, ms, s, m or h |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -what | enum | rmsd | Structural difference measure: rmsd, rho or rhosc |
| -[no]pbc | bool | yes | PBC check |
| -fit | enum | rot+trans | Fit to reference structure: rot+trans, translation or none |
| -prev | int | 0 | Compare with previous frame |
| -[no]split | bool | no | Split graph where time is zero |
| -skip | int | 1 | Only write every nr-th frame to matrix |
| -skip2 | int | 1 | Only write every nr-th frame to matrix |
| -max | real | -1 | Maximum level in comparison matrix |
| -min | real | -1 | Minimum level in comparison matrix |
| -bmax | real | -1 | Maximum level in bond angle matrix |
| -bmin | real | -1 | Minimum level in bond angle matrix |
| -nlevels | int | 80 | Number of levels in the matrices |