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g_rmsMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
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), reference Maiorov & Crippen, PROTEINS 22, 273 (1995). This is selected by -what.
Each structure from a trajectory (-f) is compared to a reference structure from a run input file by least-squares fitting the structures on top of each other. 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.
Option -prev produces the comparison with a previous frame.
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.
All the structures are fitted pairwise.
With -f2, the 'other structures' are taken from a second trajectory.
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 |
| -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 |
| -[no]X | bool | no | Use dialog box GUI to edit command line options |
| -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 |
| -[no]fit | bool | yes | Fit to reference structure |
| -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 |