NAME

       gmx-rmsf - Calculate atomic fluctuations

SYNOPSIS

          gmx rmsf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                   [-q [<.pdb>]] [-oq [<.pdb>]] [-ox [<.pdb>]] [-o [<.xvg>]]
                   [-od [<.xvg>]] [-oc [<.xvg>]] [-dir [<.log>]] [-b <time>]
                   [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]res]
                   [-[no]aniso] [-[no]fit]

DESCRIPTION

       gmx  rmsf  computes  the  root  mean square fluctuation (RMSF, i.e. standard deviation) of
       atomic positions in the trajectory (supplied with -f)  after  (optionally)  fitting  to  a
       reference frame (supplied with -s).

       With  option  -oq the RMSF values are converted to B-factor values, which are written to a
       .pdb file. By default, the coordinates in this output file are taken  from  the  structure
       file  provided  with  -s,although  you can also use coordinates read from a different .pdb
       fileprovided with -q. There is very little error checking,  so  in  this  caseit  is  your
       responsibility  to  make  sure  all  atoms  in  the structure fileand .pdb file correspond
       exactly to each other.

       Option -ox writes the B-factors to a file with the average coordinates in the trajectory.

       With the option -od the root mean square deviation with respect to the reference structure
       is calculated.

       With  the option -aniso, gmx rmsf will compute anisotropic temperature factors and then it
       will also output average coordinates and a .pdb file with ANISOU records (corresponding to
       the -oq or -ox option). Please note that the U values are orientation-dependent, so before
       comparison with experimental data you should verify  that  you  fit  to  the  experimental
       coordinates.

       When  a  .pdb input file is passed to the program and the -aniso flag is set a correlation
       plot of the Uij will be created, if any anisotropic temperature factors are present in the
       .pdb file.

       With  option -dir the average MSF (3x3) matrix is diagonalized.  This shows the directions
       in which the atoms fluctuate the most and the least.

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

       -q [<.pdb>] (eiwit.pdb) (Optional)
              Protein data bank file

       Options to specify output files:

       -oq [<.pdb>] (bfac.pdb) (Optional)
              Protein data bank file

       -ox [<.pdb>] (xaver.pdb) (Optional)
              Protein data bank file

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

       -od [<.xvg>] (rmsdev.xvg) (Optional)
              xvgr/xmgr file

       -oc [<.xvg>] (correl.xvg) (Optional)
              xvgr/xmgr file

       -dir [<.log>] (rmsf.log) (Optional)
              Log 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

       -[no]res (no)
              Calculate averages for each residue

       -[no]aniso (no)
              Compute anisotropic temperature factors

       -[no]fit (yes)
              Do a least squares superposition before computing RMSF. Without this you must  make
              sure that the reference structure and the trajectory match.

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2024, GROMACS development team