Scalable molecular dynamics with NAMD
نویسندگان
چکیده
منابع مشابه
Scalable molecular dynamics with NAMD
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, parameters, and file formats. This art...
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dynamics with NAMD on the IBM Blue Gene/L system S. Kumar C. Huang G. Zheng E. Bohm A. Bhatele J. C. Phillips H. Yu L. V. Kalé NAMD (nanoscale molecular dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes, and water molecules. In a biomolecular simulation, the problem size is fixed and a large number of ...
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Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Here we present the implementation of aMD in the parallel simulation program NAMD. We show that aMD simulations performed with NAMD have only a small overhead compared with classical MD simulations. Through examp...
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Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that provides efficient free energy calculations of biomolecules. Like the previous accelerated molecular dynamics (aMD), GaMD allows for "unconstrained" enhanced sampling without the need to set predefined collective variables and so is useful for studying complex biomolecular conformational chan...
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Computational methodologies that couple the dynamical evolution of a set of replicated copies of a system of interest offer powerful and flexible approaches to characterize complex molecular processes. Such multiple copy algorithms (MCAs) can be used to enhance sampling, compute reversible work and free energies, as well as refine transition pathways. Widely used examples of MCAs include temper...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2005
ISSN: 0192-8651,1096-987X
DOI: 10.1002/jcc.20289