namd

The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of the parallel molecular dynamics simulation program NAMD. NAMD2 is a major improvement over its predecessor, NAMD 1.5, in both computation speed and simulation features.

This release is a binary-only beta version of NAMD2. It has already received extensive testing inside our group, but we still have some additional testing and code cleanup before releasing the source. Nevertheless, we believe it to be stable, and think you will find it a significant improvement over NAMD 1.5.

Obtaining namd

NAMD2 binaries for Linux, HP-UX, Solaris, SGI Origin and the T3E are available at ftp://ftp.ks.uiuc.edu/pub/mdscope/namd2/bin/. For more information see http://www.ks.uiuc.edu/Research/namd/Namd2.html and direct questions or comments to namd@ks.uiuc.edu.

Features: namd is a molecular dynamics program designed to provide high performance simulations for large biological molecular systems. Specifically, namd achieves high performance by exploiting the power of parallel computers and by providing a modular design that facilitates the implementation of new algorithms. A high degree of modularity is obtained by using an object-oriented design and implementation in C++. namd uses spatial decomposition coupled with a multithreaded, message-driven design, which provides a scalable, efficient parallel framework. namd also incorporates the Distributed Parallel Multipole Tree Algorithm (DPMTA) developed by the Scientific Computing group at Duke University, which allows full electrostatic force evaluation in O(N) time. As part of the MDScope system, namd is connected via the communication system MDComm to the molecular graphics program VMD (also developed by the Theoretical Biophysics group) to provide such an interactive system where researchers can view and interact with a running simulation.

The program has many features, which include:

• Input and output file compatibility with X-PLOR;
  
  
• CHARMM19 and CHARMM22 parameter support;
  
  
• Support for traditional MD functions such as energy minimization, velocity rescaling, harmonic boundary conditions, harmonic atom restraints, etc.;
  
  
• Full electrostatic evaluation using DPMTA from Duke University integrated using a multiple timestep integration scheme. For more information on DPMTA, see the the Duke Scientific Computing home page at: http://www.ee.duke.edu/Research/SciComp.html
  
  
• Spatial decomposition for O(N/P) scalability of memory, computation, and communication;
  
  
• Message-driven, multithread design for high performance parallel execution;
  
  
• Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure;
  
  
• Portable parallelism provided by PVM and Charm++ communication systems;
  
  
• Integration with the program VMD, a molecular graphics program developed in the Theoretical Biophysics Group at the University of Illinois. See the VMD WWW home page for more information.

VMD can be used to set up and concurrently display a MD simulation using namd. The two programs, along with the intermediary communications package (called MDComm) constitute the 'MDScope' environment.

Availability: namd should run on any parallel platform with a C++ compiler and PVM version 3.3.6 or later. Tested Makefiles are included for clusters of HP, SGI, and IBM workstations, Cray T3D, and Convex Exemplar. Precompiled binaries are provided for HP and SGI workstations.

VMD, namd, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. This project is funded by the National Institutes of Health and the National Science Foundation.

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