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