table of contents
g_covar(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_covar(1) |
NAME¶
g_covar - calculates and diagonalizes the covariance matrixSYNOPSIS¶
g_covar -f traj.xtc -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm -xpma covara.xpm -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -xvg enum -[no]fit -[no]ref -[no]mwa -last int -[no]pbcDESCRIPTION¶
g_covar calculates and diagonalizes the (mass-weighted) covariance matrix. All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. When the fit and analysis groups are identical and the analysis is non mass-weighted, the fit will also be non mass-weighted.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
xvgr/xmgr file
Full precision trajectory: trr trj cpt
Structure file: gro g96 pdb etc.
Log file
Generic data file
X PixMap compatible matrix file
X PixMap compatible matrix 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)
Time unit: fs, ps, ns, us, ms or s
xvg plot formatting: xmgrace, xmgr or none
Fit to a reference structure
Use the deviation from the conformation in the structure file instead of from the average
Mass-weighted covariance analysis
Last eigenvector to write away (-1 is till the last)
Apply corrections for periodic boundary conditions
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |