man g_covar (Commandes) - g_covar VERSION 3.3_beta_20050823

NAME

g_covar VERSION 3.3_beta_20050823

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 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/>.