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gmx-rmsf - Calculate atomic fluctuations


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]


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

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 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)
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>
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.

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