EnglishFrenchSpanish

Ad


OnWorks favicon

gmx-nmens - Online in the Cloud

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

This is the command gmx-nmens 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

PROGRAM:

NAME


gmx-nmens - Generate an ensemble of structures from the normal modes

SYNOPSIS


gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]] [-s [<.tpr/.gro/...>]]
[-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-xvg <enum>]
[-temp <real>] [-seed <int>] [-num <int>] [-first <int>]
[-last <int>]

DESCRIPTION


gmx nmens generates an ensemble around an average structure in a subspace that is defined
by a set of normal modes (eigenvectors). The eigenvectors are assumed to be
mass-weighted. The position along each eigenvector is randomly taken from a Gaussian
distribution with variance kT/eigenvalue.

By default the starting eigenvector is set to 7, since the first six normal modes are the
translational and rotational degrees of freedom.

OPTIONS


Options to specify input files:

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

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

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

Other options:

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-temp <real> (300)
Temperature in Kelvin

-seed <int> (-1)
Random seed, -1 generates a seed from time and pid

-num <int> (100)
Number of structures to generate

-first <int> (7)
First eigenvector to use (-1 is select)

-last <int> (-1)
Last eigenvector to use (-1 is till the last)

Use gmx-nmens online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    turkdevops
    turkdevops
    TurkDevOps a�?k kaynak yaz?l?m
    geli?tirici topluluklar? DevTurks-Team
    Taraf?ndan desteklenmektedir..
    Features:https://github.com/turkdevopshttps://turkdevops.g...
    Download turkdevops
  • 2
    asammdf
    asammdf
    *asammdf* is a fast Python parser and
    editor for ASAM (Associtation for
    Standardisation of Automation and
    Measuring Systems) MDF / MF4
    (Measurement Data Format...
    Download asammdf
  • 3
    LAME (Lame Aint an MP3 Encoder)
    LAME (Lame Aint an MP3 Encoder)
    LAME is an educational tool to be used
    for learning about MP3 encoding. The
    goal of the LAME project is to improve
    the psycho acoustics, quality and speed
    of MP...
    Download LAME (Lame Aint an MP3 Encoder)
  • 4
    wxPython
    wxPython
    A set of Python extension modules that
    wrap the cross-platform GUI classes from
    wxWidgets.. Audience: Developers. User
    interface: X Window System (X11), Win32 ...
    Download wxPython
  • 5
    packfilemanager
    packfilemanager
    This is the Total War pack file manager
    project, starting from version 1.7. A
    short introduction into Warscape
    modding: ...
    Download packfilemanager
  • 6
    IPerf2
    IPerf2
    A network traffic tool for measuring
    TCP and UDP performance with metrics
    around both throughput and latency. The
    goals include maintaining an active
    iperf cod...
    Download IPerf2
  • More »

Linux commands

Ad