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)-s[<.tpr/.gro/…>] (topol.tpr)-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)-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.