1GMX-RMSF(1)                         GROMACS                        GMX-RMSF(1)
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NAME

6       gmx-rmsf - Calculate atomic fluctuations
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SYNOPSIS

9          gmx rmsf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                   [-q [<.pdb>]] [-oq [<.pdb>]] [-ox [<.pdb>]] [-o [<.xvg>]]
11                   [-od [<.xvg>]] [-oc [<.xvg>]] [-dir [<.log>]] [-b <time>]
12                   [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]res]
13                   [-[no]aniso] [-[no]fit]
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DESCRIPTION

16       gmx rmsf computes the root mean square fluctuation (RMSF, i.e. standard
17       deviation) of atomic positions in the trajectory (supplied with -f) af‐
18       ter (optionally) fitting to a reference frame (supplied with -s).
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20       With option -oq the RMSF values are converted to B-factor values, which
21       are written to a .pdb file. By default, the coordinates in this  output
22       file  are  taken  from the structure file provided with -s,although you
23       can also use coordinates read from a different .pdb  fileprovided  with
24       -q.  There is very little error checking, so in this caseit is your re‐
25       sponsibility to make sure all atoms in the structure fileand .pdb  file
26       correspond exactly to each other.
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28       Option  -ox writes the B-factors to a file with the average coordinates
29       in the trajectory.
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31       With the option -od the root mean square deviation with respect to  the
32       reference structure is calculated.
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34       With  the  option -aniso, gmx rmsf will compute anisotropic temperature
35       factors and then it will also output average  coordinates  and  a  .pdb
36       file  with  ANISOU  records  (corresponding  to the -oq or -ox option).
37       Please note that the U values are orientation-dependent, so before com‐
38       parison  with  experimental  data you should verify that you fit to the
39       experimental coordinates.
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41       When a .pdb input file is passed to the program and the -aniso flag  is
42       set  a  correlation plot of the Uij will be created, if any anisotropic
43       temperature factors are present in the .pdb file.
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45       With option -dir the average MSF (3x3) matrix  is  diagonalized.   This
46       shows  the  directions  in  which  the atoms fluctuate the most and the
47       least.
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OPTIONS

50       Options to specify input files:
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52       -f [<.xtc/.trr/...>] (traj.xtc)
53              Trajectory: xtc trr cpt gro g96 pdb tng
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55       -s [<.tpr/.gro/...>] (topol.tpr)
56              Structure+mass(db): tpr gro g96 pdb brk ent
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58       -n [<.ndx>] (index.ndx) (Optional)
59              Index file
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61       -q [<.pdb>] (eiwit.pdb) (Optional)
62              Protein data bank file
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64       Options to specify output files:
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66       -oq [<.pdb>] (bfac.pdb) (Optional)
67              Protein data bank file
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69       -ox [<.pdb>] (xaver.pdb) (Optional)
70              Protein data bank file
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72       -o [<.xvg>] (rmsf.xvg)
73              xvgr/xmgr file
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75       -od [<.xvg>] (rmsdev.xvg) (Optional)
76              xvgr/xmgr file
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78       -oc [<.xvg>] (correl.xvg) (Optional)
79              xvgr/xmgr file
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81       -dir [<.log>] (rmsf.log) (Optional)
82              Log file
83
84       Other options:
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86       -b <time> (0)
87              Time of first frame to read from trajectory (default unit ps)
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89       -e <time> (0)
90              Time of last frame to read from trajectory (default unit ps)
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92       -dt <time> (0)
93              Only use frame when t MOD dt = first time (default unit ps)
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95       -[no]w (no)
96              View output .xvg, .xpm, .eps and .pdb files
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98       -xvg <enum> (xmgrace)
99              xvg plot formatting: xmgrace, xmgr, none
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101       -[no]res (no)
102              Calculate averages for each residue
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104       -[no]aniso (no)
105              Compute anisotropic temperature factors
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107       -[no]fit (yes)
108              Do a least squares superposition before computing RMSF.  Without
109              this  you  must  make  sure that the reference structure and the
110              trajectory match.
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SEE ALSO

113       gmx(1)
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115       More    information    about    GROMACS    is    available    at     <‐
116       http://www.gromacs.org/>.
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119       2022, GROMACS development team
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1242022.2                           Jun 16, 2022                      GMX-RMSF(1)
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