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 -[no]version -nice int -b time -e time -dt time -tu enum -xvg enum -[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.

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.

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 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 

OTHER OPTIONS

-[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