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 (878/1)
Hardware (522/0)
Security (192/0)
Tutorials (345/0)
Off Topic (181/0)


User Functions
Username:

Password:

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


Events
There are no upcoming events




NAMD

NAMD

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

NAMD is written using the Charm++ parallel programming model, noted for its parallel efficiency and often used to simulate large systems (millions of atoms). NAMD is implemented using the Converse runtime system. Converse provides machine-independent interface to all popular parallel computers as well as workstation clusters.

 NAMD 2.10

Price
Free to download

Size
84MB
License

Non-Exclusive, Non-Commercial Use License

Developer
Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL)

Website
www.ks.uiuc.edu/.../namd

System Requirements
Charm++ 6.0 or higher
TCL and FFTW libraries
VMD plugins

Support:
Parallel Programming Laboratory, User Guide, Wiki, Tutorials, Mailing List

Selected Reviews:

Features include:

  • VMD used to prepare molecular structure for simulation
  • Also reads X-PLOR, CHARMM, AMBER, and GROMACS input files
  • Psfgen tool generates structure and coordinate files for CHARMM force field
  • Efficient conjugate gradient minimization
  • Fixed atoms and harmonic restraints
  • Thermal equilibration via periodic rescaling, reinitialization, or Langevin dynamics
  • Force Field Compatibility
  • Efficient Full Electrostatics Algorithms
  • Multiple Time Stepping
  • Input and Output Compatibility
  • Dynamics Simulation Options - MD simulations using options such as:
    • Constant energy dynamics
    • Constant temperature dynamics via:
      • Velocity rescaling
      • Velocity reassignment
      • Langevin dynamics
    • Periodic boundary conditions
    • Constant pressure dynamics via
      • Berendsen pressure coupling
      • Nosť-Hoover Langevin piston
    • Energy minimization
    • Fixed atoms
    • Rigid waters
    • Rigid bonds to hydrogen
    • Harmonic restraints
    • Spherical or cylindrical boundary restraints
  • Interactive molecular dynamics simulations
  • Accelerated molecular dynamics provides a robust biasing potential that increases the escape rates from potential wells, while still converging to the correct canonical distribution.
  • Load balancing
  • Shared-Memory Multicore and SMP Builds
  • Replica-based umbrella sampling via collective variables module
  • Optimized shared-memory single-node and multiple-node CUDA builds
  • CUDA GPU-accelerated generalized Born implicit solvent (GBIS) model
  • CUDA GPU-accelerated energy evaluation and minimization
  • Native CRAY XE/XK uGNI network layer implementation
  • Faster grid forces and lower-accuracy "lite" implementation
  • Hybrid MD with knowledge-based Go forces to drive folding
  • Linear combination of pairwise overlaps (LCPO) SASA for GBIS model
  • Weeks-Chandler-Anderson decomposition for alchemical FEP simulations
  • Native replica-exchange implementation for CRAY XE/XK and BlueGene/Q

NAMD in action

Return to Biology Tools Home Page

Bookmark and Share


Last Updated Wednesday, May 28 2014 @ 03:58 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
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)

  • Friday 06/13
  • 12 Remarkable Free Shell Scripting Books (0)

  • Saturday 06/07
  • Open Source LDAP Solutions (0)

  • Monday 06/02
  • Delightful ASCII Art Tools (0)

  • Saturday 05/31
  • Best Tools for Network Inventory Management (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
    4850 votes | 2 comments

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