NAME

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

       VERSION 4.6.5

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), 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  GMXLIB. 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

       -[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 2 Dec 2013                                 g_rms(1)