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Highlight: NAMD 2.10 Advances Simulations Large and Small

GlpT protein embedded in membrane

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made with VMD

The 2.10 release of the molecular dynamics program NAMD includes numerous enhancements to support simulations of massive supramolecular assemblies such as the HIV capsid (see highlight Elusive HIV-1 Capsid). A single such simulation of a hundred million atoms or more can utilize the tens of thousands of processors of petascale supercomputers thanks to recent advances in computational methodology reported here. Equally if not more significant, however, are advances in NAMD's implementation of multiple copy algorithms for enhanced sampling of smaller molecular systems as reported here and extended here. These algorithms have already allowed researchers studying the molecular machinery of living cells to reveal for the first time with NAMD mechanisms operating on timescales of milliseconds or longer, including the rotary action of the ubiquitous energy conversion complex ATP synthase and the inward to outward opening transition of the membrane transporter protein GlpT, shown in the accompanying animation. NAMD 2.10 also introduces multilevel summation, reported here, a major algorithmic advance enabling efficient long-range electrostatics for non-periodic and semi-periodic simulations. More on new features in the 2.10 release of NAMD can be found here.
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