NAME
g_rmsf - calculates atomic fluctuations
VERSION 4.0.1
SYNOPSIS
g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb
-ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir rmsf.log
-[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]res
-[no]aniso -[no]fit
DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
deviation) of atomic positions after (optionally) fitting to a
reference frame.
With option -oq the RMSF values are converted to B-factor values,
which are written to a pdb file with the coordinates, of the structure
file, or of a pdb file when -q is specified. Option -ox writes the
B-factors to a file with the average coordinates.
With the option -od the root mean square deviation with respect to the
reference structure is calculated.
With the option aniso g_rmsf will compute anisotropic temperature
factors and then it will also output average coordinates and a pdb file
with ANISOU records (corresonding to the -oq or -ox option). Please
note that the U values are orientation dependent, so before comparison
with experimental data you should verify that you fit to the
experimental coordinates.
When a pdb input file is passed to the program and the -aniso flag is
set a correlation plot of the Uij will be created, if any anisotropic
temperature factors are present in the pdb file.
With option -dir the average MSF (3x3) matrix is diagonalized. This
shows the directions in which the atoms fluctuate the most and the
least.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-q eiwit.pdb Input, Opt.
Protein data bank file
-oq bfac.pdb Output, Opt.
Protein data bank file
-ox xaver.pdb Output, Opt.
Protein data bank file
-o rmsf.xvg Output
xvgr/xmgr file
-od rmsdev.xvg Output, Opt.
xvgr/xmgr file
-oc correl.xvg Output, Opt.
xvgr/xmgr file
-dir rmsf.log Output, Opt.
Log file
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[no]resno
Calculate averages for each residue
-[no]anisono
Compute anisotropic termperature factors
-[no]fityes
Do a least squares superposition before computing RMSF. Without this
you must make sure that the reference structure and the trajectory
match.
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_rmsf(1)