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 (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 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 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.