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NAME
       gmx-rms - Calculate RMSDs with a reference structure and RMSD matrices


SYNOPSIS
          gmx rms [-s [<.tpr/.gro/...>]] [-f [<.xtc/.trr/...>]]
                  [-f2 [<.xtc/.trr/...>]] [-n [<.ndx>]] [-o [<.xvg>]]
                  [-mir [<.xvg>]] [-a [<.xvg>]] [-dist [<.xvg>]] [-m [<.xpm>]]
                  [-bin [<.dat>]] [-bm [<.xpm>]] [-b <time>] [-e <time>]
                  [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
                  [-what <enum>] [-[no]pbc] [-fit <enum>] [-prev <int>]
                  [-[no]split] [-skip <int>] [-skip2 <int>] [-max <real>]
                  [-min <real>] [-bmax <real>] [-bmin <real>] [-[no]mw]
                  [-nlevels <int>] [-ng <int>]


DESCRIPTION
       gmx  rms  compares  two structures by computing the root mean square deviation (RMSD), the
       size-independent rho similarity parameter (rho) or the scaled rho (rhosc), see  Maiorov  &
       Crippen, Proteins 22, 273 (1995).  This is selected by -what.

       Each  structure from a trajectory (-f) is compared to a reference structure. The reference
       structure is taken from the structure file (-s).

       With option -mir also a comparison with the mirror image of  the  reference  structure  is
       calculated.   This  is  useful  as  a  reference  for  'significant' values, see Maiorov &
       Crippen, Proteins 22, 273 (1995).

       Option -prev produces the comparison with a previous frame the specified number of  frames
       ago.

       Option  -m  produces a matrix in .xpm format of comparison values of each structure in the
       trajectory with respect to each other structure. This file  can  be  visualized  with  for
       instance xv and can be converted to postscript with gmx xpm2ps.

       Option  -fit  controls  the  least-squares fitting of the structures on top of each other:
       complete fit (rotation and translation), translation only, or no fitting at all.

       Option -mw controls whether mass weighting is done or  not.   If  you  select  the  option
       (default)  and  supply  a  valid  .tpr file masses will be taken from there, otherwise the
       masses will be deduced from the atommass.dat file in GMXLIB. This is  fine  for  proteins,
       but not necessarily for other molecules. A default mass of 12.011 amu (carbon) is assigned
       to unknown atoms. You can check whether this happened by turning on the  -debug  flag  and
       inspecting the log file.

       With  -f2,  the  'other  structures'  are taken from a second trajectory, this generates a
       comparison matrix of one trajectory versus the other.

       Option -bin does a binary dump of the comparison matrix.

       Option -bm produces a matrix of average  bond  angle  deviations  analogously  to  the  -m
       option. Only bonds between atoms in the comparison group are considered.


OPTIONS
       Options to specify input files:

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

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

       -f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
              Trajectory: xtc trr cpt gro g96 pdb tng

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

       Options to specify output files:

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

       -mir [<.xvg>] (rmsdmir.xvg) (Optional)
              xvgr/xmgr file

       -a [<.xvg>] (avgrp.xvg) (Optional)
              xvgr/xmgr file

       -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
              xvgr/xmgr file

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

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

       -bm [<.xpm>] (bond.xpm) (Optional)
              X PixMap compatible matrix 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)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

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

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

       -what <enum> (rmsd)
              Structural difference measure: rmsd, rho, rhosc

       -[no]pbc (yes)
              PBC check

       -fit <enum> (rot+trans)
              Fit to reference structure: rot+trans, translation, none

       -prev <int> (0)
              Compare with previous frame

       -[no]split (no)
              Split graph where time is zero

       -skip <int> (1)
              Only write every nr-th frame to matrix

       -skip2 <int> (1)
              Only write every nr-th frame to matrix

       -max <real> (-1)
              Maximum level in comparison matrix

       -min <real> (-1)
              Minimum level in comparison matrix

       -bmax <real> (-1)
              Maximum level in bond angle matrix

       -bmin <real> (-1)
              Minimum level in bond angle matrix

       -[no]mw (yes)
              Use mass weighting for superposition

       -nlevels <int> (80)
              Number of levels in the matrices

       -ng <int> (1)
              Number of groups to compute RMS between


SEE ALSO
       gmx(1)

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


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