.TH g_covar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_covar - calculates and diagonalizes the covariance matrix

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_covar\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " eigenval.xvg "
.BI "\-v" " eigenvec.trr "
.BI "\-av" " average.pdb "
.BI "\-l" " covar.log "
.BI "\-ascii" " covar.dat "
.BI "\-xpm" " covar.xpm "
.BI "\-xpma" " covara.xpm "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-xvg" " enum "
.BI "\-[no]fit" ""
.BI "\-[no]ref" ""
.BI "\-[no]mwa" ""
.BI "\-last" " int "
.BI "\-[no]pbc" ""
.SH DESCRIPTION
\&\fB g_covar\fR 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 (\fB \-v\fR).
\&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 \fB \-ref\fR 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 \fB g_anaeig\fR.
\&


\&Option \fB \-ascii\fR writes the whole covariance matrix to
\&an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
\&


\&Option \fB \-xpm\fR writes the whole covariance matrix to an \fB .xpm\fR file.
\&


\&Option \fB \-xpma\fR writes the atomic covariance matrix to an \fB .xpm\fR file,
\&i.e. for each atom pair the sum of the xx, yy and zz covariances is
\&written.
\&


\&Note that the diagonalization of a matrix requires memory and time
\&that will increase at least as fast as than the square of the number
\&of atoms involved. It is easy to run out of memory, in which
\&case this tool will probably exit with a 'Segmentation fault'. You
\&should consider carefully whether a reduced set of atoms will meet
\&your needs for lower costs.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " eigenval.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-v" " eigenvec.trr" 
.B Output
 Full precision trajectory: trr trj cpt 

.BI "\-av" " average.pdb" 
.B Output
 Structure file: gro g96 pdb etc. 

.BI "\-l" " covar.log" 
.B Output
 Log file 

.BI "\-ascii" " covar.dat" 
.B Output, Opt.
 Generic data file 

.BI "\-xpm" " covar.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-xpma" " covara.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]fit"  "yes   "
 Fit to a reference structure

.BI "\-[no]ref"  "no    "
 Use the deviation from the conformation in the structure file instead of from the average

.BI "\-[no]mwa"  "no    "
 Mass\-weighted covariance analysis

.BI "\-last"  " int" " \-1" 
 Last eigenvector to write away (\-1 is till the last)

.BI "\-[no]pbc"  "yes   "
 Apply corrections for periodic boundary conditions

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.