1GMX-RMSF(1) GROMACS GMX-RMSF(1)
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6 gmx-rmsf - Calculate atomic fluctuations
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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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16 gmx rmsf computes the root mean square fluctuation (RMSF, i.e. standard
17 deviation) of atomic positions in the trajectory (supplied with -f)
18 after (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
25 responsibility to make sure all atoms in the structure fileand .pdb
26 file 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 (corresonding 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
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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
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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 termperature 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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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 2020, GROMACS development team
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1242019.6 Feb 28, 2020 GMX-RMSF(1)