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/>.
Thu 16 Oct 2008 g_covar(1)