OnWorks favicon

gmx-nmtraj - Online in the Cloud

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

This is the command gmx-nmtraj 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-nmtraj - Generate a virtual oscillating trajectory from an eigenvector


gmx nmtraj [-s [<.tpr/.gro/...>]] [-v [<.trr/.cpt/...>]]
[-o [<.xtc/.trr/...>]] [-eignr <string>]
[-phases <string>] [-temp <real>] [-amplitude <real>]
[-nframes <int>]


gmx nmtraj generates an virtual trajectory from an eigenvector, corresponding to a
harmonic Cartesian oscillation around the average structure. The eigenvectors should
normally be mass-weighted, but you can use non-weighted eigenvectors to generate
orthogonal motions. The output frames are written as a trajectory file covering an entire
period, and the first frame is the average structure. If you write the trajectory in (or
convert to) PDB format you can view it directly in PyMol and also render a photorealistic
movie. Motion amplitudes are calculated from the eigenvalues and a preset temperature,
assuming equipartition of the energy over all modes. To make the motion clearly visible in
PyMol you might want to amplify it by setting an unrealistically high temperature.
However, be aware that both the linear Cartesian displacements and mass weighting will
lead to serious structure deformation for high amplitudes - this is is simply a limitation
of the Cartesian normal mode model. By default the selected eigenvector is set to 7, since
the first six normal modes are the translational and rotational degrees of freedom.


Options to specify input files:

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

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

Options to specify output files:

-o [<.xtc/.trr/...>] (nmtraj.xtc)
Trajectory: xtc trr gro g96 pdb tng

Other options:

-eignr <string> (7)
String of eigenvectors to use (first is 1)

-phases <string> (0.0)
String of phases (default is 0.0)

-temp <real> (300)
Temperature (K)

-amplitude <real> (0.25)
Amplitude for modes with eigenvalue<=0

-nframes <int> (30)
Number of frames to generate

Use gmx-nmtraj online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    KompoZer is a wysiwyg HTML editor using
    the Mozilla Composer codebase. As
    Nvu's development has been stopped
    in 2005, KompoZer fixes many bugs and
    adds a f...
    Download KompoZer
  • 2
    Free Manga Downloader
    Free Manga Downloader
    The Free Manga Downloader (FMD) is an
    open source application written in
    Object-Pascal for managing and
    downloading manga from various websites.
    This is a mirr...
    Download Free Manga Downloader
  • 3
    UNetbootin allows you to create bootable
    Live USB drives for Ubuntu, Fedora, and
    other Linux distributions without
    burning a CD. It runs on Windows, Linux,
    and ...
    Download UNetbootin
  • 4
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM is an easy to use
    ERP and CRM open source software package
    (run with a web php server or as
    standalone software) for businesses,
    Download Dolibarr ERP - CRM
  • 5
    SQuirreL SQL Client
    SQuirreL SQL Client
    SQuirreL SQL Client is a graphical SQL
    client written in Java that will allow
    you to view the structure of a JDBC
    compliant database, browse the data in
    Download SQuirreL SQL Client
  • 6
    Brackets is a free, modern open-source
    text editor made especially for Web
    Development. Written in HTML, CSS, and
    JavaScript with focused visual tools and
    Download Brackets
  • More »

Linux commands