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
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_rms(1)