NAMD 1.5 Release
Announcing the release of NAMD version 1.5 ------------------------------------------ The Theoretical Biophysics group of the Beckman Institute at the University of Illinois would like to announce the availability of version 1.5 of NAMD, a high-performance molecular mechanics program for simulating large biomolecular systems on parallel and distributed computers. This software is being made available to the molecular modeling community free of charge and includes commented source code and extensive documentation. New in this version ------------------- * Added features include rigid bonds and moving harmonic restraints. * Updated user guide, also available in HTML form. * Modified to work with PVM 3.4 beta. * Enhanced performance by as much as 30%. * Modified to work with the latest version of DPMTA (2.7). * Included DPMTA source to make installation easier. * Simplified build process, fewer options to specify, better documentation. * Several bug fixes. ==================== Basic information about NAMD ====================== Obtaining NAMD -------------- A more complete description of NAMD is available on the NAMD home page: http://www.ks.uiuc.edu/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd/ Email questions to namd@ks.uiuc.edu. Features -------- Efficient full electrostatics: NAMD incorporates the Distributed Parallel Multipole Tree Algorithm (DPMTA) developed by the Scientific Computing Group at Duke University to provide full electrostatic interactions in O(N) time. To further reduce the computational cost, DPMTA is integrated using a multiple timestep integration scheme which computes full electrostatic interactions only periodically during the simulation. Scalable parallelism: NAMD has an efficient parallel design that allows large systems to scale well to many processors. The use of a spatial decomposition scheme combined with message-driven execution achieves load balance and the overlap of communication and computation. Modifiable: A major design goal of NAMD is to allow researchers to implement new algorithms and techniques easily. To achieve this, NAMD design and implementation is fully documented in the NAMD Programming Guide. NAMD has an object-oriented design implemented in C++ to provide a high degree of modularity and data abstraction. Portable: For communication, NAMD uses PVM (Parallel Virtual Machine) from Oak Ridge National Laboratory, which has itself been ported to most architectures. Porting NAMD is then simply a matter of having PVM and a reasonable C++ compiler. We have successfully ported NAMD to all of our UNIX machines, which include HP, SGI, Sun, and Linux, both single processor and shared memory multiprocessor. Compatibility with X-PLOR: The input and output files used by NAMD are identical to those used by the program X-PLOR. Thus, simulations can be easily migrated between the two packages, allowing the output of NAMD to be analyzed using X-PLOR or any other tool built for these file formats. Standard MD features: NAMD implements standard molecular dynamics features such as energy minimization, velocity rescaling, spherical boundary conditions, harmonic constraints, and Langevin dynamics. Requirements ------------ * UNIX with C and C++ compilers. * PVM (http://www.epm.ornl.gov/pvm/pvm_home.html). * For generating required PSF structure files, we recommend X-PLOR (http://xplor.csb.yale.edu/xplor-info/xplor-info.html). ========================================================================== Theoretical Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign David Hardy namd@ks.uiuc.edu September 4, 1998
