g_rmsf(1)

NAME
g_rmsf VERSION 3.2.0

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 -nice int -b time -e time -dt time -[no]w -[no]res -[no]aniso

DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after first 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.

FILES
-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb -s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb xml -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 no
 Print help info and quit -nice int 19
 Set the nicelevel -b time -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]w no
 View output xvg, xpm, eps and pdb files -[no]res no
 Calculate averages for each residue -[no]aniso no
 Compute anisotropic termperature factors