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NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions,(More)
Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scal-able program. It is also(More)
NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoffelectrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an(More)
Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational(More)
Achieving good scaling for fine-grained communication intensive applications on modern supercomputers remains challenging. In our previous work, we have shown that such an application --- NAMD --- scales well on the full Jaguar XT5 without long-range interactions; Yet, with them, the speedup falters beyond 64K cores. Although the new Gemini interconnect on(More)
Graphics Processing UnitsVpowerful, programmable, and highly parallelVare increasingly targeting general-purpose computing applications. ABSTRACT | The graphics processing unit (GPU) has become an integral part of today's mainstream computing systems. Over the past six years, there has been a marked increase in the performance and capabilities of GPUs. The(More)
Large-scale GPU clusters are gaining popularity in the scientific computing community. However, their deployment and production use are associated with a number of new challenges. In this paper, we present our efforts to address some of the challenges with building and running GPU clusters in HPC environments. We touch upon such issues as balanced cluster(More)
NAMD is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique now used by most scalable programs for biomolecular simulations, including Blue Matter and Desmond developed by IBM and D. E. Shaw respectively. NAMD has been developed using Charm++ and benefits from its(More)
Accurate electrostatic descriptions of aqueous solvent are critical for simulation studies of bio-molecules, but the computational cost of explicit treatment of solvent is very high. A computationally more feasible alternative is a generalized Born implicit solvent description which models polar solvent as a dielectric continuum. Unfortunately, the(More)
Human apolipoprotein A-1 (apo A-1) is the major protein component of high-density lipoproteins. The apo A-1 lipid-binding domain was used as a template for the synthesis of amphipathic helical proteins termed membrane scaffold proteins, employed to self-assemble soluble monodisperse discoidal particles called Nanodiscs. In these particles, membrane scaffold(More)