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gmx-rmsdist(1)                  GROMACS Manual                  gmx-rmsdist(1)

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

SYNOPSIS
       gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
                   [-n [<.ndx>]] [-equiv [<.dat>]] [-o [<.xvg>]]
                   [-rms [<.xpm>]] [-scl [<.xpm>]] [-mean [<.xpm>]]
                   [-nmr3 [<.xpm>]] [-nmr6 [<.xpm>]] [-noe [<.dat>]]
                   [-nice <int>] [-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/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.:

       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 and output files:

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

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

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

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

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

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

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

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

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

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

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

       Other options:

       -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]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
       gromacs(7)

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

VERSION 5.0.6                                                   gmx-rmsdist(1)