Main Table of Contents

Thu 26 Aug 2010


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.


-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]h gmx_bool no Print help info and quit
-[no]version gmx_bool no 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]w gmx_bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]res gmx_bool no Calculate averages for each residue
-[no]aniso gmx_bool no Compute anisotropic termperature factors
-[no]fit gmx_bool yes Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.