g_rmsf(1)

NAME

g_rmsf - calculates atomic fluctuations

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

DESCRIPTION

g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after first 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

Generic trajectory: xtc trr trj gro g96 pdb

-s topol.tpr Input

Structure+mass(db): tpr tpb tpa gro g96 pdb xml

-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]h no

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]w no

View output xvg, xpm, eps and pdb files

-[no]xvgr yes

Add specific codes (legends etc.) in the output xvg files for the

xmgrace program

-[no]res no

Calculate averages for each residue

-[no]aniso no

Compute anisotropic termperature factors

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.

Mon 29 Aug 2005 g_rmsf(1)