g_rmsf

Main Table of Contents

VERSION 4.6.4
Wed 13 Nov 2013


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 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

optionfilenametypedescription
-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

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


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