Provided by: gromacs-data_2020-2build1_all
gmx-rmsf - Calculate atomic fluctuations
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]
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 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.
gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>.
2020, GROMACS development team