1 .TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_rmsf - calculates atomic fluctuations
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-q" " eiwit.pdb "
12 .BI "\-oq" " bfac.pdb "
13 .BI "\-ox" " xaver.pdb "
14 .BI "\-o" " rmsf.xvg "
15 .BI "\-od" " rmsdev.xvg "
16 .BI "\-oc" " correl.xvg "
17 .BI "\-dir" " rmsf.log "
19 .BI "\-[no]version" ""
30 \&\fB g_rmsf\fR computes the root mean square fluctuation (RMSF, i.e. standard
31 \&deviation) of atomic positions in the trajectory (supplied with \fB \-f\fR)
32 \&after (optionally) fitting to a reference frame (supplied with \fB \-s\fR).
35 \&With option \fB \-oq\fR the RMSF values are converted to B\-factor
36 \&values, which are written to a \fB .pdb\fR file with the coordinates, of the
37 \&structure file, or of a \fB .pdb\fR file when \fB \-q\fR is specified.
38 \&Option \fB \-ox\fR writes the B\-factors to a file with the average
42 \&With the option \fB \-od\fR the root mean square deviation with
43 \&respect to the reference structure is calculated.
46 \&With the option \fB \-aniso\fR, \fB g_rmsf\fR will compute anisotropic
47 \&temperature factors and then it will also output average coordinates
48 \&and a \fB .pdb\fR file with ANISOU records (corresonding to the \fB \-oq\fR
49 \&or \fB \-ox\fR option). Please note that the U values
50 \&are orientation\-dependent, so before comparison with experimental data
51 \&you should verify that you fit to the experimental coordinates.
54 \&When a \fB .pdb\fR input file is passed to the program and the \fB \-aniso\fR
56 \&a correlation plot of the Uij will be created, if any anisotropic
57 \&temperature factors are present in the \fB .pdb\fR file.
60 \&With option \fB \-dir\fR the average MSF (3x3) matrix is diagonalized.
61 \&This shows the directions in which the atoms fluctuate the most and
66 Trajectory: xtc trr trj gro g96 pdb cpt
68 .BI "\-s" " topol.tpr"
70 Structure+mass(db): tpr tpb tpa gro g96 pdb
72 .BI "\-n" " index.ndx"
76 .BI "\-q" " eiwit.pdb"
78 Protein data bank file
80 .BI "\-oq" " bfac.pdb"
82 Protein data bank file
84 .BI "\-ox" " xaver.pdb"
86 Protein data bank file
92 .BI "\-od" " rmsdev.xvg"
96 .BI "\-oc" " correl.xvg"
100 .BI "\-dir" " rmsf.log"
106 Print help info and quit
108 .BI "\-[no]version" "no "
109 Print version info and quit
111 .BI "\-nice" " int" " 19"
114 .BI "\-b" " time" " 0 "
115 First frame (ps) to read from trajectory
117 .BI "\-e" " time" " 0 "
118 Last frame (ps) to read from trajectory
120 .BI "\-dt" " time" " 0 "
121 Only use frame when t MOD dt = first time (ps)
124 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
126 .BI "\-xvg" " enum" " xmgrace"
127 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
129 .BI "\-[no]res" "no "
130 Calculate averages for each residue
132 .BI "\-[no]aniso" "no "
133 Compute anisotropic termperature factors
135 .BI "\-[no]fit" "yes "
136 Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.
141 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.