g_rms(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					  g_rms(1)

NAME

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

       VERSION 4.5.4-dev-20110404-bc5695c

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 -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -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), transla-
       tion 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  GMXLIB. This is fine for proteins, but not neces-
       sarily for other molecules. A default mass of 12.011 amu (carbon) is assigned to unknown atoms. You can check whether this happend by turn-
       ing 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

       -[no]versionno
	Print version 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:  fs,  ps,  ns,  us,	ms or  s

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

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -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/>.

								  Mon 4 Apr 2011							  g_rms(1)