Provided by: gromacs-data_4.6.5-1build1_all
g_covar - calculates and diagonalizes the covariance matrix VERSION 4.6.5
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]pbc
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. The eigenvectors are written to a trajectory file ( -v). When the same atoms are used for the fit and the covariance analysis, the reference structure for the fit is written first with t=-1. The average (or reference when -ref is used) structure is written with t=0, the eigenvectors are written as frames with the eigenvector number as timestamp. The eigenvectors can be analyzed with g_anaeig. Option -ascii writes the whole covariance matrix to an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ... Option -xpm writes the whole covariance matrix to an .xpm file. Option -xpma writes the atomic covariance matrix to an .xpm file, i.e. for each atom pair the sum of the xx, yy and zz covariances is written. Note that the diagonalization of a matrix requires memory and time that will increase at least as fast as than the square of the number of atoms involved. It is easy to run out of memory, in which case this tool will probably exit with a 'Segmentation fault'. You should consider carefully whether a reduced set of atoms will meet your needs for lower costs.
-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 -o eigenval.xvg Output xvgr/xmgr file -v eigenvec.trr Output Full precision trajectory: trr trj cpt -av average.pdb Output Structure file: gro g96 pdb etc. -l covar.log Output Log file -ascii covar.dat Output, Opt. Generic data file -xpm covar.xpm Output, Opt. X PixMap compatible matrix file -xpma covara.xpm Output, Opt. X PixMap compatible matrix file
-[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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]fityes Fit to a reference structure -[no]refno Use the deviation from the conformation in the structure file instead of from the average -[no]mwano Mass-weighted covariance analysis -last int -1 Last eigenvector to write away (-1 is till the last) -[no]pbcyes Apply corrections for periodic boundary conditions
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_covar(1)