LinuxLinks.com
Newbies What Next ? News Forums Calendar

Search





News Sections
Home
General News (3973/0)
Reviews (628/0)
Press Releases (464/0)
Distributions (187/0)
Software (882/2)
Hardware (522/0)
Security (192/0)
Tutorials (345/0)
Off Topic (181/1)


User Functions
Username:

Password:

Don't have an account yet? Sign up as a New User


Events
There are no upcoming events




GROMACS

GROMACS

GROMACS is a molecular dynamics simulator, with building and analysis tools.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

It provides extremely high performance compared to other competitors. A lot of algorithmic optimizations have been introduced in the code. The software is normally 3-10 times faster than any other program.

There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases.

 GROMACS 5.0.2

Price
Free to download

Size
25.1MB
License

GNU GPL v2

Developer
David van der Spoel, Berk Hess, Erik Lindahl, and many contributors

Website
www.gromacs.org

System Requirements
10MB space (using shared libraries)

Support:
Wiki, Tutorials, HOWTOs, Mailing Lists, Facebook

Selected Reviews:
Journal of Computational Chemistry

Features include:

  • User-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong
  • There is no scripting language - all programs use a simple interface with command line options for input and output files
  • Extensive manuals provided free of charge in electronic or paper format.
  • Integrated graphical user interface available for all programs
  • As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and what time and date it expects to be finished
  • Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision. All files from GROMACS 2.0 can further be used in the new version 3
  • Write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user
  • Large selection of flexible tools for trajectory analysis - you won't have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place
  • A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats
  • Can be run in parallel, using standard MPI communication
  • Contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail
  • Includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules

Return to Scientific Home Page | Return to Biology Tools Home Page

Bookmark and Share


Last Updated Tuesday, October 14 2014 @ 02:16 PM EDT


We have written a range of guides highlighting excellent free books for popular programming languages. Check out the following guides: C, C++, C#, Java, JavaScript, CoffeeScript, HTML, Python, Ruby, Perl, Haskell, PHP, Lisp, R, Prolog, Scala, Scheme, Forth, SQL, Node.js (new), Fortran (new), Erlang (new), Pascal (new), and Ada (new).


Group Tests
All Group Tests

Top Free Software
5 Office Suites
7 Document Processors
6 Lean Desktops
6 Desktop Search
9 Project Management
9 Groupware Apps
14 File Managers
10 Databases
21 Backup Tools
21 DVD Tools
21 Window Managers
21 Productivity Tools
9 Terminal Emulators
21 Financial Tools
21 Text Editors
21 Video Emulators
21 Home Emulators
42 Graphics Apps
6 CAD Apps
42 Scientific Apps
10 Web Browsers
42 Email Apps
12 Instant Messaging
10 IRC Clients
7 Twitter Clients
12 News Aggregators
11 VoIP Apps
11 Remote Display Apps
42 Best Games
42 More Games
21 More Games
21 Notable Games (1)
21 Notable Games (2)
21 Notable Games (3)
8 ASCII Games
9 Educational Games
42 Audio Apps
42 Video Apps
6 Screencasting Apps
80 Security Apps
9 System Monitoring
6 Family History Apps
11 PDF Tools
6 Music Servers
6 Collection Managers
7 Calculator Apps
8 Geometry Apps
Free Console Apps
14 Multimedia
Programming
8 Compilers
9 IDEs
9 Debuggers
7 Revision Control Apps
6 Doc Generators
'Free' Proprietary
21 Closed-Source Apps
Top Commercial Apps
42 Games
Free Web Software
21 Web CMS
14 Wiki Engines
8 Blog Apps
6 eCommerce Apps
5 Human Resource Apps
10 ERP
10 CRM
6 Data Warehouse Apps
8 Business Intelligence
6 Point-of-Sale

All Group Tests

Other Articles
Migrating from Windows
Back up your data
Distribution Guide
Distro Portal Pages
20 Free Linux Books
Running Linux Under Windows


Older Stories
Sunday 08/31
  • Low-Spec Hardware? Try these Desktop Environments (0)

  • Monday 08/25
  • Powerful Command-line File Transfer Programs (0)

  • Saturday 08/16
  • Great Apps to Take Notes (0)

  • Sunday 08/10
  • Exciting New Terminal Emulators (0)

  • Saturday 08/02
  • The Best Lightweight Graphical Email Clients (0)

  • Sunday 07/20
  • Excellent Free Distraction-Free Tools for Writers (0)
  • Pick of the Bunch: Console Internet Applications (0)
  • Mobile Phone Management Made Easy (0)

  • Saturday 06/28
  • Easy File Comparisons With These Great Free Diff Tools (0)
  • 9 ASCII Games You'll Want to Play Again and Again (0)


  • Vote

    What do you find MOST attractive about Open Source software?

    Amount of customization
    Security
    Freedom provided
    Speed of development
    Quality
    Multiple versions
    Cost
    Potential to contribute
    Ability to modify code
    Results
    4872 votes | 2 comments

    Built with GeekLog and phpBB
    Comments to the webmaster are welcome
    Copyright 2009 LinuxLinks.com - All rights reserved