g_rmsf - calculates atomic fluctuations
VERSION 4.6.3
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
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 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.
−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
−[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.
More information about GROMACS is available at <http://www.gromacs.org/>.