M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. NAMD { A parallel, object-oriented molecular dynamics program. Int. J. Supercomput. Appl. High Perform. Comput., 10:251-268, 1996.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....is already very small for very low temperatures; e.g. for a Ca 40 Coulomb crystal at 1 K the wavelength is of order 10 m, a factor 50 100 smaller than the typical separation distance. sizes certain macroscopic properties of matter can be studied. There is a proliferation of programs for MD [4, 14, 30, 31, 32, 53, 77, 81, 86, 91, 98, 108, 110, 119, 124, 125] and several of these are robust production codes; some with scalable parallel implementations. They cover common MD problems and are excellent tools to perform simulations. However, many of the codes are legacy programs that are either poorly organized or extremely complex. One important factor ....

....dominate, since the integration is relatively cheap to carry out. Nevertheless, the terms of the sum of interactions U( x 1 ; x 2 ; x N ) are independent. Altogether, this makes MD to a certain extent inherently parallel.This has been exploited by several parallel MD programs [4, 14, 22, 23, 32, 53, 77, 81, 86, 91, 98, 110, 124, 125]. When parallelizing MD, there are two important considerations to make. First, the MD program must perform well for a small number of particles, i.e. less than 1000. There are several interests to carry out simulations with a few thousand particles over a long time scale, e.g. a protein ....

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M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. NAMD -- A parallel, object-oriented molecular dynamics program. Int. J. Supercomput. Applics. High Performance Computing, 10(4):251--268, Winter 1996.

....steps. Parallelizing such a dynamic simulation requires that the decomposition be adjusted periodically to ensure the equitable distribution of work. The use of a spatial decomposition for MD has become widespread in recent years. It is used by AMBER [3, 11] Charmm [7] Gromos [4] and NAMD [10], all of which run in a message passing paradigm, as opposed to our shared memory implementation. In general, each of these implementations found good scaling properties, but it is difficult to compare overall performance of the parallel MD simulators, as machine speeds have improved significantly ....

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert D. Skeel, and Klaus Schulten. NAMD - a parallel, object-oriented molecular dynamics program. Journal of Supercomputing Applications and High Performance Computing, In press.

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M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. NAMD---a parallel, object-oriented molecular dynamics program. Intl. J. Supercomput. Applics. High Performance Computing, 10:251--268, 1996.

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M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. NAMD---a parallel, objectoriented molecular dynamics program. Intl. J. Supercomput. Applics. High Performance Computing, 10(4):251--268, Winter 1996.

....processors. Not all computations are globally synchronous. Divide and conquer computations, and the state space search computations lead to computations trees, where the only dependencies are between parent and child nodes of the tree. Consider a molecular dynamics application (such as NAMD [13]) which divides the simulation volume into cells distributed among various processors. Computation for each cell may depend only on data from adjacent cells during a single timestep. However, over a period of several steps, the data from a particular cell indirectly a#ects every other cell in the ....

....half of their time waiting for results from the busy processor. Thus, even though we have lost only 1 16th of the total computational power to the outside job, the performance of the program drops by fifty percent We have observed this e#ect while running a parallel molecular dynamics application [13]. To study this phenomenon further, we implemented an artificial benchmark that allows us to study the phenomenon without the complexities of a full featured code. Our benchmark is a simple simulation. The computational domain is a two dimensional square, which is divided into a uniform ....

M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. NAMD--- A parallel, object-oriented molecular dynamics program. J. Supercomputing App., 1996.

....is running with a high parallel e# ciency, and one doubles the size of molecule as well as the number of processors, one is assured that there will be the same number of boxes per processor and, therefore, the same parallel efficiency. This method was used in the earlier version of our program [29] As other researchers have noted, load imbalance can be a severe problem for SD, especially for simulating non periodic systems. NAMD addressed this problem by assigning the force computations corresponding to a pair of neighboring cubes (called patches in NAMD) to the patch on a processor with ....

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert D. Skeel, and Klaus Schulten. NAMD -- A parallel, object-oriented molecular dynamics program. J. Supercomputing App., 10:251--268, 1996.

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Mark Nelson. Namd - a parallel, object-oriented molecular dynamics program. Master's thesis, University of Illinois at Urbana Champaign, 1995.

....implementation (MPICH from Argonne National Laboratory 2 ) to their new cluster con guration, to take advantage of the BProc subsystem. MPI programs should compile and run under this modi ed MPICH installation with little or no modi cation. 3 Not (Just) Another Molecular Dynamics Program NAMD [1] is a parallel molecular dynamics program developed at the University of Illinois at Urbana Champaign. Its purpose is to simulate biologically interesting molecules with the goal of gaining insight into their behavior and function. Prominent features of NAMD include: usage of the CHARMM force ....

M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. Skeel and K. Schulten. NAMD - A parallel, object-oriented molecular dynamics program. J. Supercomputing App., 10:251-268, 1996.

....is arbitrarily increased. More sophisticated strategies, which are variants of force decomposition ( 6, 12] 4 are also non scalable in this sense, although in practice they may lead to reasonable speedups on medium size computers (up to 128 processors) Spatial decomposition schemes (used in [11, 13]) where atoms are distributed into cubes depending on the spatial locations, and migrated among the cubes as needed, are shown to be theoretically scalable. For a more detailed analysis of scalability, see [9] The variant of spatial decomposition we propose uses cubes whose dimensions are ....

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert D. Skeel, and Klaus Schulten. NAMD---a parallel, object-oriented molecular dynamics program. Intl. J. Supercomput. Applics. High Performance Computing, 10(4):251--268, Winter 1996.

....order energy 2nd order Figure 1: Energy and various truncations of modified Hamiltonians for decalanine. by (9) The unmodified Hamiltonians are those of classical molecular dynamics. The testing was done with a molecular dynamics program written by the second author, which is compatible with NAMD [11, 16] but limited in features to facilitate algorithm testing. The first couple of experiments demonstrate the quality of the modified Hamiltonians. The test problem is a 66 atom peptide, decalanine, in a vacuum [1] The force field parameters are those of CHARMM 22 for proteins [13, 14] without ....

M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kal'e, R. D. Skeel, and K. Schulten. NAMD---a parallel, object-oriented molecular dynamics program. Intl. J. Supercomput. Applics. High Performance Computing, 10(4):251--268, Winter 1996.

....require data from neighboring regions, atomic data can be fetched once and then reused many times, due to the similarities of interactions of nearby atoms. The use of a spatial decomposition for MD has become widespread in recent years. It is used by AMBER [3, 9] Charmm [6] Gromos [4] and NAMD [8], all of which run in a message passing paradigm, as opposed to our shared memory implementation. In general, each of these implementations found good scaling properties, but it is difficult to compare overall performance of the parallel MD simulators, as machine speeds have improved significantly ....

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert D. Skeel, and Klaus Schulten. NAMD - a parallel, object-oriented molecular dynamics program. Journal of Supercomputing Applications and High Performance Computing, In press.

....migratable objects, which are supported in Charm [7] a C based parallel programming system. It relies on actual measurement of time spent by each object, instead of predictions of their computational load, to achieve an efficient load distribution. 2 NAMD: A Molecular Dynamics Program NAMD [8] is the production quality molecular dynamics program we are developing in the Theoretical Biophysics group at the University of Illinois. From inception, it has been designed to be a scalable parallel program. The latest version, NAMD 2 implements a new load balancing scheme to achieve our ....

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal'e, Robert D. Skeel, and Klaus Schulten. NAMD--- A parallel, object-oriented molecular dynamics program. Intl. J. Supercomput. Applics. High Performance Computing, 10(4):251--268, Winter 1996.

....used for NAMD implementation are described in section 4. Section 5 describes the design of key NAMD components in detail and illustrates the use of multilingual modules. Preliminary performance results are given in section 6. 2 Previous Work: PVM based NAMD NAMD is a major component of MDSCOPE [13], being developed as a part of the interdisciplinary project on biomolecular modeling led by Prof. K. Schulten, Prof. L.V. Kale, and Prof. R.D. Skeel. NAMD models the behavior of a molecule by simulating the motions of the constituent atoms in a small region of its environment. Each atom is acted ....

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal'e, Robert D. Skeel, and Klaus Schulten. NAMD--- A parallel, object-oriented molecular dynamics program. J. Supercomputing App., 1996.

....scheduler of Converse is made available to Perl programs to schedule computations received from remote processors. For common programming tasks such as analyzing the log information of a WWW server, we have obtained a near linear speedup using mdPerl. 4 Multilingual Programming: Applications NAMD [19] is a parallel molecular dynamics simulation program being developed with the Theoretical Biophysics group at the University of Illinois. NAMD simulates the motions of biological molecules such as proteins and DNA by repeatedly computing the forces exerted by individual atoms on one another, and ....

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal'e, Robert D. Skeel, and Klaus Schulten. NAMD--- A parallel, object-oriented molecular dynamics program. Intl. J. Supercomput. Applics. High Performance Computing, 10(4):251--268, Winter 1996.

.... automatic differentiation of parallel programs written in explicitly parallel languages, like Fortran M [4] or using parallel extensions, such as MPI and PVM [5, 8] We are applying some of these techniques to NAMD, a parallel molecular dynamics application written in C with PVM message passing [12]. This paper describes the automatic differentiation of NAMD. We begin with a brief introduction to automatic differentiation in Section 2. Section 3 briefly describes NAMD and explains which derivatives are being computed and how they will be used. Section 4 describes how AD technology is being ....

.... The ADIC tool has processed programs of over 10,000 lines and the ADIFOR tool has been applied to programs of over 100,000 lines [2] 3 NAMD NAMD is a parallel, object oriented molecular dynamics program designed for high performance molecular dynamics simulations of large biomolecular systems [12]. Important features include scalable parallelism, an efficient implementation of full electrostatics, modifiability, portability, and compatibility with X PLOR (a program for determining threedimensional structures from crystallographic diffraction or NMR data) Full electrostatics are computed ....

M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten, NAMD - a parallel, object-oriented molecular dynamics program, Journal of Supercomputing Applications and High Performance Computing. In Press.

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M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. NAMD { A parallel, object-oriented molecular dynamics program. Int. J. Supercomput. Appl. High Perform. Comput., 10:251-268, 1996.

No context found.

M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. NAMD -- A parallel, object-oriented molecular dynamics program. Int. J. Supercomput. Appl. High Perform. Comput., 10:251--268, 1996.

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