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| GMX-RMSF(1) | GROMACS | GMX-RMSF(1) |
NAME
gmx-rmsf - Calculate atomic fluctuationsSYNOPSIS
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.
SEE ALSO
gmx(1)More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2022, GROMACS development team| January 14, 2022 | 2021.5 |
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