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

Generic trajectory: xtc trr trj gro g96 pdb

-s topol.tpr Input

Structure+mass(db): tpr tpb tpa gro g96 pdb xml

-n index.ndx Input, Opt.

Index file

-o eigenval.xvg Output

xvgr/xmgr file

-v eigenvec.trr Output

Full precision trajectory: trr trj

-av average.pdb Output

Generic structure: gro g96 pdb xml

-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]h no

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 , s , m or h

-[no]xvgr yes

Add specific codes (legends etc.) in the output xvg files for the

xmgrace program

-[no]fit yes

Fit to a reference structure

-[no]ref no

Use the deviation from the conformation in the structure file instead

of from the average

-[no]mwa no

Mass-weighted covariance analysis

-last int -1

Last eigenvector to write away (-1 is till the last)

-[no]pbc yes

Apply corrections for periodic boundary conditions

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.

Mon 29 Aug 2005 g_covar(1)