g_rms_d (1) - Linux Manuals

g_rms_d: calculates rmsd's with a reference structure and rmsd matrices

NAME

g_rms - calculates rmsd's with a reference structure and rmsd matrices

VERSION 4.0.1

SYNOPSIS

g_rms -s topol.tpr -f traj.xtc -f2 traj.xtc -n index.ndx -o rmsd.xvg -mir rmsdmir.xvg -a avgrp.xvg -dist rmsd-dist.xvg -m rmsd.xpm -bin rmsd.dat -bm bond.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -what enum -[no]pbc -fit enum -prev int -[no]split -skip int -skip2 int -max real -min real -bmax real -bmin real -[no]mw -nlevels int -ng int

DESCRIPTION

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.

Option -mw controls whether mass weighting is done or not. If you select the option (default) and supply a valid tpr file masses will be taken from there, otherwise the masses will be deduced from the atommass.dat file in the GROMACS library directory. This is fine for proteins but not necessarily for other molecules. A default mass of 12.011 amu (Carbon) is assigned to unknown atoms. You can check whether this happend by turning on the -debug flag and inspecting the log file.

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.

FILES

-s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

-f traj.xtc Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

-f2 traj.xtc Input, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

-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 

OTHER OPTIONS

-[no]hno
 Print help 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)

-tu enum ps
 Time unit:  ps,  fs,  ns,  us,  ms or  s

-[no]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-what enum rmsd
 Structural difference measure:  rmsd,  rho or  rhosc

-[no]pbcyes
 PBC check

-fit enum rot+trans
 Fit to reference structure:  rot+trans,  translation or  none

-prev int 0
 Compare with previous frame

-[no]splitno
 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

-[no]mwyes
 Use mass weighting for superposition

-nlevels int 80
 Number of levels in the matrices

-ng int 1
 Number of groups to compute RMS between