Main Table of Contents

Thu 26 Aug 2010


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.


-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]h gmx_bool no Print help info and quit
-[no]version gmx_bool no 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]fit gmx_bool yes Fit to a reference structure
-[no]ref gmx_bool no Use the deviation from the conformation in the structure file instead of from the average
-[no]mwa gmx_bool no Mass-weighted covariance analysis
-last int -1 Last eigenvector to write away (-1 is till the last)
-[no]pbc gmx_bool yes Apply corrections for periodic boundary conditions