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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)