1GMX-COVAR(1) GROMACS GMX-COVAR(1)
2
6 gmx-covar - Calculate and diagonalize the covariance matrix
7
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
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.
22 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.
29 The eigenvectors can be analyzed with gmx anaeig.
31 Option -ascii writes the whole covariance matrix to an ASCII file. The
33 order of the elements is: x1x1, x1y1, x1z1, x1x2, …
34 Option -xpm writes the whole covariance matrix to an .xpm file.
36 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.
39 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.
46
48 Options to specify input files:
49 -f [<.xtc/.trr/…>] (traj.xtc)
51 Trajectory: xtc trr cpt gro g96 pdb tng
52 -s [<.tpr/.gro/…>] (topol.tpr)
54 Structure+mass(db): tpr gro g96 pdb brk ent
55 -n [<.ndx>] (index.ndx) (Optional)
57 Index file
58 Options to specify output files:
60 -o [<.xvg>] (eigenval.xvg)
62 xvgr/xmgr file
63 -v [<.trr/.cpt/…>] (eigenvec.trr)
65 Full precision trajectory: trr cpt tng
66 -av [<.gro/.g96/…>] (average.pdb)
68 Structure file: gro g96 pdb brk ent esp
69 -l [<.log>] (covar.log)
71 Log file
72 -ascii [<.dat>] (covar.dat) (Optional)
74 Generic data file
75 -xpm [<.xpm>] (covar.xpm) (Optional)
77 X PixMap compatible matrix file
78 -xpma [<.xpm>] (covara.xpm) (Optional)
80 X PixMap compatible matrix file
81 Other options:
83 -b <time> (0)
85 Time of first frame to read from trajectory (default unit ps)
86 -e <time> (0)
88 Time of last frame to read from trajectory (default unit ps)
89 -dt <time> (0)
91 Only use frame when t MOD dt = first time (default unit ps)
92 -tu <enum> (ps)
94 Unit for time values: fs, ps, ns, us, ms, s
95 -xvg <enum> (xmgrace)
97 xvg plot formatting: xmgrace, xmgr, none
98 -[no]fit (yes)
100 Fit to a reference structure
101 -[no]ref (no)
103 Use the deviation from the conformation in the structure file
104 instead of from the average
105 -[no]mwa (no)
107 Mass-weighted covariance analysis
108 -last <int> (-1)
110 Last eigenvector to write away (-1 is till the last)
111 -[no]pbc (yes)
113 Apply corrections for periodic boundary conditions
114
116 gmx(1)
117 More information about GROMACS is available at <‐
119 http://www.gromacs.org/>.
120
122 2019, GROMACS development team
1232019.4 Oct 02, 2019 GMX-COVAR(1)