g_rmsf_d (1) - Linux Manuals

g_rmsf_d: calculates atomic fluctuations


g_rmsf - calculates atomic fluctuations



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]xvgr -[no]res -[no]aniso -[no]fit


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


-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 


 Print help 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)

 View output xvg, xpm, eps and pdb files

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

 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.



More information about GROMACS is available at <http://www.gromacs.org/>.