NAME

       g_rmsdist - calculates atom pair distances averaged with power -2, -3 or -6

       VERSION 4.6.5

SYNOPSIS

       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  -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -nlevels int -max
       real -[no]sumh -[no]pbc

DESCRIPTION

        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.

FILES

       -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

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)

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

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

       -nlevels int 40
        Discretize RMS in this number of levels

       -max real -1
        Maximum level in matrices

       -[no]sumhyes
        Average distance over equivalent hydrogens

       -[no]pbcyes
        Use periodic boundary conditions when computing distances

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                          Mon 2 Dec 2013                             g_rmsdist(1)