g_rmsf(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rmsf(1)
NAME
g_rmsf - calculates atomic fluctuations
VERSION 4.5.4-dev-20110404-bc5695c
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 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]res -[no]aniso -[no]fit
DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with -f)
after (optionally) fitting to a reference frame (supplied with -s).
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 com-
parison 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 aniso-
tropic 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
-[no]versionno
Print version 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
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-[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/>.
Mon 4 Apr 2011 g_rmsf(1)