Millisecond-scale molecular dynamics simulations on Anton

Shaw, David E.; Dror, Ron O.; Salmon, John K.; Grossman, J. P.; MacKenzie, Kenneth; Bank, Joseph A.; Young, Cliff; Deneroff, Martin M.; Batson, Brannon; Bowers, K. J.; Chow, Edmond; Eastwood, Michael P.; Ierardi, Douglas J.; Klepeis, John L.; Kuskin, Jeffrey S.; Larson, Richard H.; Lindorff‐Larsen, Kresten; Maragakis, Paul; Moraes, Mark A.; Piana, Stefano; Shan, Yibing; Towles, Brian

doi:10.1145/1654059.1654099

Cited by 278 publications

(303 citation statements)

References 35 publications

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“…1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 However, due to high computational demands, equilibrium MD is currently limited to tens of microseconds on standard supercomputers and hundreds of microseconds on special purpose machines. 97 Importantly, enhanced sampling methods can be employed to obtain equilibrium properties over longer timescales, including conformation changes underlying channel gating. [98][99][100][101] MD-based methods also exist to compute thermodynamic information that may be useful to correlate experimental observables such as single channel conductance or thermodynamics with structural conformational changes.…”

Section: Identifying a Trp Specific Thermosensormentioning

confidence: 99%

Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors

et al. 2015

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Transient receptor potential (TRP) ion channels are eukaryotic polymodal sensors that function as molecular cellular signal integrators. TRP family members sense and are modulated by a wide array of inputs, including temperature, pressure, pH, voltage, chemicals, lipids, and other proteins. These inputs induce signal transduction events mediated by nonselective cation passage through TRP channels. In this review, we focus on the thermosensitive TRP channels and highlight the emerging view that these channels play a variety of significant roles in physiology and pathophysiology in addition to sensory biology. We attempt to use this viewpoint as a framework to understand the complexity and controversy of TRP channel modulation and ultimately suggest that the complex functional behavior arises inherently because this class of protein is exquisitely sensitive to many diverse and distinct signal inputs. To illustrate this idea, we primarily focus on TRP channel thermosensing. We also offer a structural, biochemical, biophysical, and computational perspective that may help to bring more coherence and consensus in understanding the function of this important class of proteins.

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Section: Identifying a Trp Specific Thermosensormentioning

confidence: 99%

Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors

et al. 2015

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“…FiP35 is still about an order of magnitude slower than the fastest folding helical protein domain of comparable size. 16 Using very long molecular dynamics (MD) simulations executed on special-purpose hardware, 17 we have recently simulated the reversible folding of FiP35 with full atomic resolution. 18 The unprecedented length of these simulations allowed us to observe multiple folding and unfolding transitions at the protein's melting temperature (Fig.…”

mentioning

confidence: 99%

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

Piana

Sarkar

Lindorff‐Larsen

et al. 2011

Journal of Molecular Biology

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162

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“…This section focuses on those parts of the Anton hardware that are relevant to the FFT; for a more general description, see the earlier papers on Anton [1]- [4]. An Anton machine is built from nodes wired together in a 3D torus; this paper reports results for 8×8×8 and 4×4×4 configurations.…”

Section: Anton Hardwarementioning

confidence: 99%

A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton

Young

Bank

Dror

et al. 2009

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis

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Anton, a massively parallel special-purpose machine for molecular dynamics simulations, performs a 32×32×32 FFT in 3.7 microseconds and a 64×64×64 FFT in 13.3 microseconds on a configuration with 512 nodes-an order of magnitude faster than all other FFT implementations of which we are aware. Achieving this FFT performance requires a coordinated combination of computation and communication techniques that leverage Anton's underlying hardware mechanisms. Most significantly, Anton's communication subsystem provides over 300 gigabits per second of bandwidth per node, message latency in the hundreds of nanoseconds, and support for word-level writes and single-ended communication. In addition, Anton's general-purpose computation system incorporates primitives that support the efficient parallelization of small 1D FFTs. Although Anton was designed specifically for molecular dynamics simulations, a number of the hardware primitives and software implementation techniques described in this paper may also be applicable to the acceleration of FFTs on general-purpose high-performance machines.

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Millisecond-scale molecular dynamics simulations on Anton

Cited by 278 publications

References 35 publications

Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors

Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton

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