gmx-rmsf - Calculate atomic fluctuations

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                       GMX-RMSF(1)

gmxrmsf 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,  gmxrmsf  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.

       gmx-rmsf - Calculate atomic fluctuations

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb 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.

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

          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]