g_rmsf (1) Linux Manual Page

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 (3×3) 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/>.