NAME

       gmx-rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6

SYNOPSIS

          gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                      [-equiv [<.dat>]] [-o [<.xvg>]] [-rms [<.xpm>]]
                      [-scl [<.xpm>]] [-mean [<.xpm>]] [-nmr3 [<.xpm>]]
                      [-nmr6 [<.xpm>]] [-noe [<.dat>]] [-b <time>] [-e <time>]
                      [-dt <time>] [-[no]w] [-xvg <enum>] [-nlevels <int>]
                      [-max <real>] [-[no]sumh] [-[no]pbc]

DESCRIPTION

       gmx  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  gmx  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.

       gmx  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/r^3  and
       1/r^6  averaging).  Finally,  lists  of  atom pairs with 1/r^3 and 1/r^6 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.:

       HB* 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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       -equiv [<.dat>] (equiv.dat) (Optional)
              Generic data file

       Options to specify output files:

       -o [<.xvg>] (distrmsd.xvg)
              xvgr/xmgr file

       -rms [<.xpm>] (rmsdist.xpm) (Optional)
              X PixMap compatible matrix file

       -scl [<.xpm>] (rmsscale.xpm) (Optional)
              X PixMap compatible matrix file

       -mean [<.xpm>] (rmsmean.xpm) (Optional)
              X PixMap compatible matrix file

       -nmr3 [<.xpm>] (nmr3.xpm) (Optional)
              X PixMap compatible matrix file

       -nmr6 [<.xpm>] (nmr6.xpm) (Optional)
              X PixMap compatible matrix file

       -noe [<.dat>] (noe.dat) (Optional)
              Generic data file

       Other options:

       -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]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum>
              xvg plot formatting: xmgrace, xmgr, none

       -nlevels <int> (40)
              Discretize RMS in this number of levels

       -max <real> (-1)
              Maximum level in matrices

       -[no]sumh (yes)
              Average distance over equivalent hydrogens

       -[no]pbc (yes)
              Use periodic boundary conditions when computing distances

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team