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       g_rmsdist - calculates atom pair distances averaged with power 2, -3 or

       VERSION 4.0.1


       g_rmsdist -f traj.xtc -s topol.tpr -n  index.ndx  -equiv  equiv.dat  -o
       distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3
       nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -nice int -b time  -e  time
       -dt time -[no]w -[no]xvgr -nlevels int -max real -[no]sumh


       g_rmsdist  computes  the  root mean square deviation of atom distances,
       which has the advantage that no fit is  needed  like  in  standard  RMS
       deviation  as computed by g_rms.  The reference structure is taken from
       the structure file.  The rmsd at time t is calculated as the rms of the
       differences  in  distance between atom-pairs in the reference structure
       and the structure at time t.

       g_rmsdist can also produce matrices of the rms distances, rms distances
       scaled  with the mean distance and the mean distances and matrices with
       NMR averaged distances (1/r3 and 1/r6  averaging).  Finally,  lists  of
       atom  pairs  with  1/r3  and  1/r6  averaged distance below the maximum
       distance ( -max, which will  default  to  0.6  in  this  case)  can  be
       generated, by default averaging over equivalent hydrogens (all triplets
       of hydrogens named *[123]). Additionally a list of equivalent atoms can
       be  supplied  ( -equiv), each line containing a set of equivalent atoms
       specified as residue number and name and atom name; e.g.:

        3 SER  HB1 3 SER  HB2

       Residue and atom names must exactly match those in the structure  file,
       including case. Specifying non-sequential atoms is undefined.


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

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

       -n index.ndx Input, Opt.
        Index file

       -equiv equiv.dat Input, Opt.
        Generic data file

       -o distrmsd.xvg Output
        xvgr/xmgr file

       -rms rmsdist.xpm Output, Opt.
        X PixMap compatible matrix file

       -scl rmsscale.xpm Output, Opt.
        X PixMap compatible matrix file

       -mean rmsmean.xpm Output, Opt.
        X PixMap compatible matrix file

       -nmr3 nmr3.xpm Output, Opt.
        X PixMap compatible matrix file

       -nmr6 nmr6.xpm Output, Opt.
        X PixMap compatible matrix file

       -noe noe.dat Output, Opt.
        Generic data file


        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)

        View output xvg, xpm, eps and pdb files

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -nlevels int 40
        Discretize rms in  levels

       -max real -1
        Maximum level in matrices

        average distance over equivalent hydrogens



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                   g_rmsdist(1)