1g_covar(1)                GROMACS suite, VERSION 4.5                g_covar(1)
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NAME

6       g_covar - calculates and diagonalizes the covariance matrix
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8       VERSION 4.5
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SYNOPSIS

11       g_covar -f traj.xtc -s topol.tpr -n index.ndx -o eigenval.xvg -v eigen‐
12       vec.trr -av average.pdb -l covar.log -ascii  covar.dat  -xpm  covar.xpm
13       -xpma covara.xpm -[no]h -[no]version -nice int -b time -e time -dt time
14       -tu enum -xvg enum -[no]fit -[no]ref -[no]mwa -last int -[no]pbc
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DESCRIPTION

17        g_covar calculates and  diagonalizes  the  (mass-weighted)  covariance
18       matrix.   All  structures  are fitted to the structure in the structure
19       file.  When this is not a run input file periodicity will not be  taken
20       into  account.  When  the fit and analysis groups are identical and the
21       analysis is non mass-weighted, the fit will also be non  mass-weighted.
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25       The eigenvectors are written to a trajectory file ( -v).  When the same
26       atoms are used for the fit and the covariance analysis,  the  reference
27       structure for the fit is written first with t=-1.  The average (or ref‐
28       erence when  -ref is used) structure is written with t=0, the eigenvec‐
29       tors are written as frames with the eigenvector number as timestamp.
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32       The eigenvectors can be analyzed with  g_anaeig.
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35       Option  -ascii writes the whole covariance matrix to an ASCII file. The
36       order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
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39       Option  -xpm writes the whole covariance matrix to an xpm file.
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42       Option  -xpma writes the atomic covariance matrix to an xpm file,  i.e.
43       for each atom pair the sum of the xx, yy and zz covariances is written.
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FILES

46       -f traj.xtc Input
47        Trajectory: xtc trr trj gro g96 pdb cpt
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49       -s topol.tpr Input
50        Structure+mass(db): tpr tpb tpa gro g96 pdb
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52       -n index.ndx Input, Opt.
53        Index file
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55       -o eigenval.xvg Output
56        xvgr/xmgr file
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58       -v eigenvec.trr Output
59        Full precision trajectory: trr trj cpt
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61       -av average.pdb Output
62        Structure file: gro g96 pdb etc.
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64       -l covar.log Output
65        Log file
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67       -ascii covar.dat Output, Opt.
68        Generic data file
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70       -xpm covar.xpm Output, Opt.
71        X PixMap compatible matrix file
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73       -xpma covara.xpm Output, Opt.
74        X PixMap compatible matrix file
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OTHER OPTIONS

78       -[no]hno
79        Print help info and quit
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81       -[no]versionno
82        Print version info and quit
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84       -nice int 19
85        Set the nicelevel
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87       -b time 0
88        First frame (ps) to read from trajectory
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90       -e time 0
91        Last frame (ps) to read from trajectory
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93       -dt time 0
94        Only use frame when t MOD dt = first time (ps)
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96       -tu enum ps
97        Time unit:  fs,  ps,  ns,  us,  ms or  s
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99       -xvg enum xmgrace
100        xvg plot formatting:  xmgrace,  xmgr or  none
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102       -[no]fityes
103        Fit to a reference structure
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105       -[no]refno
106        Use  the deviation from the conformation in the structure file instead
107       of from the average
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109       -[no]mwano
110        Mass-weighted covariance analysis
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112       -last int -1
113        Last eigenvector to write away (-1 is till the last)
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115       -[no]pbcyes
116        Apply corrections for periodic boundary conditions
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SEE ALSO

120       gromacs(7)
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122       More  information  about  GROMACS  is  available  at   <http://www.gro‐
123       macs.org/>.
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127                                Thu 26 Aug 2010                     g_covar(1)