1GMX-COVAR(1)                        GROMACS                       GMX-COVAR(1)
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NAME

6       gmx-covar - Calculate and diagonalize the covariance matrix
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SYNOPSIS

9          gmx covar [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                    [-o [<.xvg>]] [-v [<.trr/.cpt/...>]]
11                    [-av [<.gro/.g96/...>]] [-l [<.log>]] [-ascii [<.dat>]]
12                    [-xpm [<.xpm>]] [-xpma [<.xpm>]] [-b <time>] [-e <time>]
13                    [-dt <time>] [-tu <enum>] [-xvg <enum>] [-[no]fit]
14                    [-[no]ref] [-[no]mwa] [-last <int>] [-[no]pbc]
15

DESCRIPTION

17       gmx  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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23       The  eigenvectors are written to a trajectory file (-v).  When the same
24       atoms are used for the fit and the covariance analysis,  the  reference
25       structure for the fit is written first with t=-1.  The average (or ref‐
26       erence when -ref is used) structure is written with t=0, the  eigenvec‐
27       tors  are  written as frames with the eigenvector number and eigenvalue
28       as step number and timestamp, respectively.
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30       The eigenvectors can be analyzed with gmx anaeig.
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32       Option -ascii writes the whole covariance matrix to an ASCII file.  The
33       order of the elements is: x1x1, x1y1, x1z1, x1x2, …
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35       Option -xpm writes the whole covariance matrix to an .xpm file.
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37       Option  -xpma writes the atomic covariance matrix to an .xpm file, i.e.
38       for each atom pair the sum of the xx, yy and zz covariances is written.
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40       Note that the diagonalization of a matrix requires memory and time that
41       will  increase  at  least  as  fast as than the square of the number of
42       atoms involved. It is easy to run out of memory,  in  which  case  this
43       tool  will  probably  exit with a ‘Segmentation fault’. You should con‐
44       sider carefully whether a reduced set of atoms will meet your needs for
45       lower costs.
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OPTIONS

48       Options to specify input files:
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50       -f [<.xtc/.trr/…>] (traj.xtc)
51              Trajectory: xtc trr cpt gro g96 pdb tng
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53       -s [<.tpr/.gro/…>] (topol.tpr)
54              Structure+mass(db): tpr gro g96 pdb brk ent
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56       -n [<.ndx>] (index.ndx) (Optional)
57              Index file
58
59       Options to specify output files:
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61       -o [<.xvg>] (eigenval.xvg)
62              xvgr/xmgr file
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64       -v [<.trr/.cpt/…>] (eigenvec.trr)
65              Full precision trajectory: trr cpt tng
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67       -av [<.gro/.g96/…>] (average.pdb)
68              Structure file: gro g96 pdb brk ent esp
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70       -l [<.log>] (covar.log)
71              Log file
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73       -ascii [<.dat>] (covar.dat) (Optional)
74              Generic data file
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76       -xpm [<.xpm>] (covar.xpm) (Optional)
77              X PixMap compatible matrix file
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79       -xpma [<.xpm>] (covara.xpm) (Optional)
80              X PixMap compatible matrix file
81
82       Other options:
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84       -b <time> (0)
85              Time of first frame to read from trajectory (default unit ps)
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87       -e <time> (0)
88              Time of last frame to read from trajectory (default unit ps)
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90       -dt <time> (0)
91              Only use frame when t MOD dt = first time (default unit ps)
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93       -tu <enum> (ps)
94              Unit for time values: fs, ps, ns, us, ms, s
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96       -xvg <enum> (xmgrace)
97              xvg plot formatting: xmgrace, xmgr, none
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99       -[no]fit (yes)
100              Fit to a reference structure
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102       -[no]ref (no)
103              Use  the  deviation  from the conformation in the structure file
104              instead of from the average
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106       -[no]mwa (no)
107              Mass-weighted covariance analysis
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109       -last <int> (-1)
110              Last eigenvector to write away (-1 is till the last)
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112       -[no]pbc (yes)
113              Apply corrections for periodic boundary conditions
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SEE ALSO

116       gmx(1)
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118       More    information    about    GROMACS    is    available    at     <‐
119       http://www.gromacs.org/>.
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122       2019, GROMACS development team
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1272019.2                           Apr 16, 2019                     GMX-COVAR(1)
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