1 .TH g_rmsf 1 "Thu 16 Oct 2008"
3 g_rmsf - calculates atomic fluctuations
10 .BI "-n" " index.ndx "
11 .BI "-q" " eiwit.pdb "
12 .BI "-oq" " bfac.pdb "
13 .BI "-ox" " xaver.pdb "
15 .BI "-od" " rmsdev.xvg "
16 .BI "-oc" " correl.xvg "
17 .BI "-dir" " rmsf.log "
29 g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
30 deviation) of atomic positions
31 after (optionally) fitting to a reference frame.
36 the RMSF values are converted to B-factor
37 values, which are written to a pdb file with the coordinates, of the
38 structure file, or of a pdb file when
43 writes the B-factors to a file with the average
49 the root mean square deviation with
50 respect to the reference structure is calculated.
55 g_rmsf will compute anisotropic
56 temperature factors and then it will also output average coordinates
57 and a pdb file with ANISOU records (corresonding to the
62 option). Please note that the U values
63 are orientation dependent, so before comparison with experimental data
64 you should verify that you fit to the experimental coordinates.
67 When a pdb input file is passed to the program and the
71 a correlation plot of the Uij will be created, if any anisotropic
72 temperature factors are present in the pdb file.
77 the average MSF (3x3) matrix is diagonalized.
78 This shows the directions in which the atoms fluctuate the most and
83 Trajectory: xtc trr trj gro g96 pdb cpt
87 Structure+mass(db): tpr tpb tpa gro g96 pdb
95 Protein data bank file
99 Protein data bank file
101 .BI "-ox" " xaver.pdb"
103 Protein data bank file
109 .BI "-od" " rmsdev.xvg"
113 .BI "-oc" " correl.xvg"
117 .BI "-dir" " rmsf.log"
123 Print help info and quit
125 .BI "-nice" " int" " 19"
128 .BI "-b" " time" " 0 "
129 First frame (ps) to read from trajectory
131 .BI "-e" " time" " 0 "
132 Last frame (ps) to read from trajectory
134 .BI "-dt" " time" " 0 "
135 Only use frame when t MOD dt = first time (ps)
138 View output xvg, xpm, eps and pdb files
140 .BI "-[no]xvgr" "yes "
141 Add specific codes (legends etc.) in the output xvg files for the xmgrace program
144 Calculate averages for each residue
146 .BI "-[no]aniso" "no "
147 Compute anisotropic termperature factors
149 .BI "-[no]fit" "yes "
150 Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.