g_rmsf

VERSION 4.6.3
Fri 5 Jul 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

option	filename	type	description
`-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

option	type	default	description
`-[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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