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 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]res -[no]aniso -[no]fit

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

-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

-[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.