g_rmsf(1)

1g_rmsf(1)                 GROMACS suite, VERSION 4.5                 g_rmsf(1)
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NAME

6       g_rmsf - calculates atomic fluctuations
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8       VERSION 4.5
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SYNOPSIS

11       g_rmsf  -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb
12       -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg  -dir  rmsf.log
13       -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum
14       -[no]res -[no]aniso -[no]fit
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DESCRIPTION

17       g_rmsf computes the root mean square fluctuation (RMSF,  i.e.  standard
18       deviation)  of  atomic positions after (optionally) fitting to a refer‐
19       ence frame.
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22       With option  -oq the RMSF values  are  converted  to  B-factor  values,
23       which  are written to a pdb file with the coordinates, of the structure
24       file, or of a pdb file when  -q is specified.  Option  -ox  writes  the
25       B-factors to a file with the average coordinates.
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28       With the option  -od the root mean square deviation with respect to the
29       reference structure is calculated.
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32       With the option  aniso g_rmsf will compute anisotropic temperature fac‐
33       tors  and  then  it will also output average coordinates and a pdb file
34       with ANISOU records (corresonding to the  -oq or  -ox  option).  Please
35       note  that the U values are orientation dependent, so before comparison
36       with experimental data you should verify that you fit to the experimen‐
37       tal coordinates.
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40       When  a pdb input file is passed to the program and the  -aniso flag is
41       set a correlation plot of the Uij will be created, if  any  anisotropic
42       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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FILES

50       -f traj.xtc Input
51        Trajectory: xtc trr trj gro g96 pdb cpt
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53       -s topol.tpr Input
54        Structure+mass(db): tpr tpb tpa gro g96 pdb
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56       -n index.ndx Input, Opt.
57        Index file
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59       -q eiwit.pdb Input, Opt.
60        Protein data bank file
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62       -oq bfac.pdb Output, Opt.
63        Protein data bank file
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65       -ox xaver.pdb Output, Opt.
66        Protein data bank file
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68       -o rmsf.xvg Output
69        xvgr/xmgr file
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71       -od rmsdev.xvg Output, Opt.
72        xvgr/xmgr file
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74       -oc correl.xvg Output, Opt.
75        xvgr/xmgr file
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77       -dir rmsf.log Output, Opt.
78        Log file
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OTHER OPTIONS

82       -[no]hno
83        Print help info and quit
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85       -[no]versionno
86        Print version info and quit
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88       -nice int 19
89        Set the nicelevel
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91       -b time 0
92        First frame (ps) to read from trajectory
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94       -e time 0
95        Last frame (ps) to read from trajectory
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97       -dt time 0
98        Only use frame when t MOD dt = first time (ps)
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100       -[no]wno
101        View output xvg, xpm, eps and pdb files
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103       -xvg enum xmgrace
104        xvg plot formatting:  xmgrace,  xmgr or  none
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106       -[no]resno
107        Calculate averages for each residue
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109       -[no]anisono
110        Compute anisotropic termperature factors
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112       -[no]fityes
113        Do  a  least squares superposition before computing RMSF. Without this
114       you must make sure that the  reference  structure  and  the  trajectory
115       match.
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO