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 with the coordinates, of the structure file, or of a .pdb file when -q is specified. Option -ox writes the B-factors to a file with the average coordinates.
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:
Options to specify output files:
Other options: