2021 · 121 citations · 32 references
Natural SciencesBiologyHigh-performance ComputingComputational BiologyComputational ChemistryDrug DiscoveryComputational ModelingHardware AccelerationMolecular SimulationBiomolecular SimulationComputational Molecular ModelingCritical QuestionsHigh-throughput ComputationMolecular Simulation AlgorithmsSupercomputer Architecture
Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA, proteins, and drug molecules). Anton 3 achieves order-of-magnitude improvements in time-to-solution over its predecessor, Anton 2 (the current state of the art), and is over 100-fold faster than any other currently available supercomputer, thereby enabling broad new avenues of research on critical questions in biology and drug discovery. This speedup means that a 512-node Anton 3 simulates a million atoms at over 100 microseconds per day. Furthermore, Anton 3 attains this performance while consuming an order of magnitude less energy per simulated microsecond than any other machine. Like its predecessors, Anton 3 was designed from the ground up around a new custom chip to best exploit the capabilities offered by new technologies. We present here the main architectural and algorithmic developments that were necessary to achieve such significant advances.
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CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki et al. · Nature Methods · 2016 · 7.6K citations · Full text