g_covar (1) - Linux Man Pages

g_covar: calculates and diagonalizes the covariance matrix

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/>.