g_covar(1)

NAME
g_covar - calculates and diagonalizes the covariance matrix VERSION 4.0.1

SYNOPSIS
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 -nice int -b time -e time -dt time -tu enum -[no]xvgr -[no]fit -[no]ref -[no]mwa -last int -[no]pbc

DESCRIPTION
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.

FILES
-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 -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

OTHER OPTIONS
-[no]hno
 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) -tu enum ps
 Time unit: ps, fs, ns, us, ms or s -[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[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

SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.