gmx rmsf#

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.