OnWorks favicon

gmx-covar - Online in the Cloud

Run gmx-covar in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmx-covar that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



gmx-covar - Calculate and diagonalize the covariance matrix


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


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

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 reference when -ref is used) structure is written with t=0,
the eigenvectors 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
consider carefully whether a reduced set of atoms will meet your needs for lower costs.


Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:

-o [<.xvg>] (eigenval.xvg)
xvgr/xmgr file

-v [<.trr/.cpt/...>] (eigenvec.trr)
Full precision trajectory: trr cpt tng

-av [<.gro/.g96/...>] (average.pdb)
Structure file: gro g96 pdb brk ent esp

-l [<.log>] (covar.log)
Log file

-ascii [<.dat>] (covar.dat) (Optional)
Generic data file

-xpm [<.xpm>] (covar.xpm) (Optional)
X PixMap compatible matrix file

-xpma [<.xpm>] (covara.xpm) (Optional)
X PixMap compatible matrix file

Other options:

-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)
Unit for time values: fs, ps, ns, us, ms, s

-xvg <enum>
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

-[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

Use gmx-covar online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Clover EFI bootloader
    Clover EFI bootloader
    Project has moved to
    Features:Boot macOS, Windows, and Linux
    in UEFI or legacy mode on Mac or PC with
    Download Clover EFI bootloader
  • 2
    Join us in Gitter!
    Enable the URPMS repository in your
    system -
    Download unitedrpms
  • 3
    Boost C++ Libraries
    Boost C++ Libraries
    Boost provides free portable
    peer-reviewed C++ libraries. The
    emphasis is on portable libraries which
    work well with the C++ Standard Library.
    See http://www.bo...
    Download Boost C++ Libraries
  • 4
    VirtualGL redirects 3D commands from a
    Unix/Linux OpenGL application onto a
    server-side GPU and converts the
    rendered 3D images into a video stream
    with which ...
    Download VirtualGL
  • 5
    Library to enable user space
    application programs to communicate with
    USB devices. Audience: Developers, End
    Users/Desktop. Programming Language: C.
    Download libusb
  • 6
    SWIG is a software development tool
    that connects programs written in C and
    C++ with a variety of high-level
    programming languages. SWIG is used with
    Download SWIG
  • More »

Linux commands