From owner-chemistry "-at-" ccl.net Tue Jul 4 13:39:30 1995 Received: from london.ks.uiuc.edu for bishop %! at !% london.ks.uiuc.edu by www.ccl.net (8.6.10/930601.1506) id NAA25004; Tue, 4 Jul 1995 13:25:03 -0400 Received: from riga.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.16/16.2) id AA140328703; Tue, 4 Jul 1995 12:25:03 -0500 From: Tom Connor Bishop Message-Id: <199507041725.AA140328703 (+ at +) london.ks.uiuc.edu> Received: by riga.ks.uiuc.edu (NX5.67d/NX3.0X) id AA06373; Tue, 4 Jul 95 12:25:02 -0500 Date: Tue, 4 Jul 95 12:25:02 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: CHEMISTRY #*at*# ccl.net Subject: Announcing the Program NAMD, Version 1.0 Reply-To: bishop (- at -) london.ks.uiuc.edu Announcing the Program namd --------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability the program namd, a new package for high performance parallel molecular dynamics simulations. This software is being made available to the structural biology research community free of charge, and includes the source code for namd, documentation, and precompiled binaries for various parallel platforms The documentation, in postscript form, includes a programmers guide and a users guide. Obtaining namd ------------- A more complete description of namd is available via the namd WWW home page: http://www.ks.uiuc.edu:1250/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd 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: o Input and output file compatibility with X-PLOR o CHARMM19 and CHARMM22 parameter support o Support for traditional MD functions such as energy minimization, velocity rescaling, harmonic boundary conditions, harmonic atom restraints, etc. o Full electrostatic evaluation using DPMTA from Duke University integrated using a multiple timestep integration scheme. For more information on DPMTA, see the Scientific Computing home page at: http://www.ee.duke.edu/Research/SciComp.html o Spatial decomposition for O(N/P) scalability of memory, computation, and communication. o Message-driven, multithread design for high performance parallel execution. o Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure. o Portable parallelism provided by PVM and Charm++ communication systems o 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 info: http://www.ks.uiuc.edu:1250/Research/vmd 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.