1 .TH g_covar 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_covar - calculates and diagonalizes the covariance matrix
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " eigenval.xvg "
12 .BI "\-v" " eigenvec.trr "
13 .BI "\-av" " average.pdb "
14 .BI "\-l" " covar.log "
15 .BI "\-ascii" " covar.dat "
16 .BI "\-xpm" " covar.xpm "
17 .BI "\-xpma" " covara.xpm "
19 .BI "\-[no]version" ""
32 \&\fB g_covar\fR calculates and diagonalizes the (mass\-weighted)
34 \&All structures are fitted to the structure in the structure file.
35 \&When this is not a run input file periodicity will not be taken into
36 \&account. When the fit and analysis groups are identical and the analysis
37 \&is non mass\-weighted, the fit will also be non mass\-weighted.
41 \&The eigenvectors are written to a trajectory file (\fB \-v\fR).
42 \&When the same atoms are used for the fit and the covariance analysis,
43 \&the reference structure for the fit is written first with t=\-1.
44 \&The average (or reference when \fB \-ref\fR is used) structure is
45 \&written with t=0, the eigenvectors
46 \&are written as frames with the eigenvector number as timestamp.
50 \&The eigenvectors can be analyzed with \fB g_anaeig\fR.
54 \&Option \fB \-ascii\fR writes the whole covariance matrix to
55 \&an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
59 \&Option \fB \-xpm\fR writes the whole covariance matrix to an xpm file.
63 \&Option \fB \-xpma\fR writes the atomic covariance matrix to an xpm file,
64 \&i.e. for each atom pair the sum of the xx, yy and zz covariances is
69 Trajectory: xtc trr trj gro g96 pdb cpt
71 .BI "\-s" " topol.tpr"
73 Structure+mass(db): tpr tpb tpa gro g96 pdb
75 .BI "\-n" " index.ndx"
79 .BI "\-o" " eigenval.xvg"
83 .BI "\-v" " eigenvec.trr"
85 Full precision trajectory: trr trj cpt
87 .BI "\-av" " average.pdb"
89 Structure file: gro g96 pdb etc.
91 .BI "\-l" " covar.log"
95 .BI "\-ascii" " covar.dat"
99 .BI "\-xpm" " covar.xpm"
101 X PixMap compatible matrix file
103 .BI "\-xpma" " covara.xpm"
105 X PixMap compatible matrix file
109 Print help info and quit
111 .BI "\-[no]version" "no "
112 Print version info and quit
114 .BI "\-nice" " int" " 19"
117 .BI "\-b" " time" " 0 "
118 First frame (ps) to read from trajectory
120 .BI "\-e" " time" " 0 "
121 Last frame (ps) to read from trajectory
123 .BI "\-dt" " time" " 0 "
124 Only use frame when t MOD dt = first time (ps)
126 .BI "\-tu" " enum" " ps"
127 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
129 .BI "\-xvg" " enum" " xmgrace"
130 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
132 .BI "\-[no]fit" "yes "
133 Fit to a reference structure
135 .BI "\-[no]ref" "no "
136 Use the deviation from the conformation in the structure file instead of from the average
138 .BI "\-[no]mwa" "no "
139 Mass\-weighted covariance analysis
141 .BI "\-last" " int" " \-1"
142 Last eigenvector to write away (\-1 is till the last)
144 .BI "\-[no]pbc" "yes "
145 Apply corrections for periodic boundary conditions
150 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.