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gmx-rmsf(1)                     GROMACS Manual                     gmx-rmsf(1)

NAME
       gmx-rmsf - Calculate atomic fluctuations

SYNOPSIS
       gmx rmsf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
                [-q [<.pdb>]] [-oq [<.pdb>]] [-ox [<.pdb>]] [-o [<.xvg>]]
                [-od [<.xvg>]] [-oc [<.xvg>]] [-dir [<.log>]] [-nice <int>]
                [-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 with the coordinates, of the structure file,
       or of a .pdb file when -q is specified. Option -ox writes the B-factors
       to a file with the average coordinates.

       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 (corresonding 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 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

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

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

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

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

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

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

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

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

       -[no]aniso  (no)
           Compute anisotropic termperature 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
       gromacs(7)

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

VERSION 5.0.6                                                      gmx-rmsf(1)