EnglishFrenchSpanish

Ad


OnWorks favicon

gmx-mdmat - Online in the Cloud

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

This is the command gmx-mdmat 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-mdmat - Calculate residue contact maps

SYNOPSIS


gmx mdmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-mean [<.xpm>]] [-frames [<.xpm>]] [-no [<.xvg>]]
[-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
[-t <real>] [-nlevels <int>]

DESCRIPTION


gmx mdmat makes distance matrices consisting of the smallest distance between residue
pairs. With -frames, these distance matrices can be stored in order to see differences in
tertiary structure as a function of time. If you choose your options unwisely, this may
generate a large output file. By default, only an averaged matrix over the whole
trajectory is output. Also a count of the number of different atomic contacts between
residues over the whole trajectory can be made. The output can be processed with gmx
xpm2ps to make a PostScript (tm) plot.

OPTIONS


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:

-mean [<.xpm>] (dm.xpm)
X PixMap compatible matrix file

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

-no [<.xvg>] (num.xvg) (Optional)
xvgr/xmgr 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)

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

-t <real> (1.5)
trunc distance

-nlevels <int> (40)
Discretize distance in this number of levels

Use gmx-mdmat online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    KompoZer
    KompoZer
    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
    UNetbootin
    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,
    foundations...
    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
    tables...
    Download SQuirreL SQL Client
  • 6
    Brackets
    Brackets
    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
    prepr...
    Download Brackets
  • More »

Linux commands

Ad