gmx-covar(1) GROMACS Manual gmx-covar(1)NAMEgmx-covar - Calculate and diagonalize the covariance matrix
SYNOPSIS
gmx covar [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-o [<.xvg>]] [-v [<.trr/.cpt/...>]]
[-av [<.gro/.g96/...>]] [-l [<.log>]] [-ascii [<.dat>]]
[-xpm [<.xpm>]] [-xpma [<.xpm>]] [-nice <int>] [-b <time>]
[-e <time>] [-dt <time>] [-tu <enum>] [-xvg <enum>]
[-[no]fit] [-[no]ref] [-[no]mwa] [-last <int>] [-[no]pbc]
DESCRIPTION
gmx covar 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 (-v). 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 ref‐
erence when -ref is used) structure is written with t=0, the eigenvec‐
tors are written as frames with the eigenvector number as timestamp.
The eigenvectors can be analyzed with gmx anaeig.
Option -ascii writes the whole covariance matrix to an ASCII file. The
order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
Option -xpm writes the whole covariance matrix to an .xpm file.
Option -xpma writes the atomic covariance matrix to an .xpm 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 con‐
sider carefully whether a reduced set of atoms will meet your needs for
lower costs.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xvg>] (eigenval.xvg) (Output)
xvgr/xmgr file
-v [<.trr/.cpt/...>] (eigenvec.trr) (Output)
Full precision trajectory: trr cpt trj tng
-av [<.gro/.g96/...>] (average.pdb) (Output)
Structure file: gro g96 pdb brk ent esp
-l [<.log>] (covar.log) (Output)
Log file
-ascii [<.dat>] (covar.dat) (Output, Optional)
Generic data file
-xpm [<.xpm>] (covar.xpm) (Output, Optional)
X PixMap compatible matrix file
-xpma [<.xpm>] (covara.xpm) (Output, Optional)
X PixMap compatible matrix file
Other options:
-nice <int> (19)
Set the nicelevel
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (ps)
-tu <enum> (ps)
Time unit: fs, ps, ns, us, ms, s
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]fit (yes)
Fit to a reference structure
-[no]ref (no)
Use the deviation from the conformation in the structure file
instead of from the average
-[no]mwa (no)
Mass-weighted covariance analysis
-last <int> (-1)
Last eigenvector to write away (-1 is till the last)
-[no]pbc (yes)
Apply corrections for periodic boundary conditions
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-covar(1)
