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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

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

       -xvg <enum> (xmgrace)
              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

       2020, GROMACS development team