table of contents
g_rmsf(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_rmsf(1) |
NAME¶
g_rmsf - calculates atomic fluctuationsSYNOPSIS¶
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]fitDESCRIPTION¶
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).FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
Protein data bank file
Protein data bank file
Protein data bank file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Log file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Calculate averages for each residue
Compute anisotropic termperature factors
Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |