J
Justin Gullingsrud
Researcher at D. E. Shaw Research
Publications - 5
Citations - 278
Justin Gullingsrud is an academic researcher from D. E. Shaw Research. The author has contributed to research in topics: Parallel algorithm & Hybrid Monte Carlo. The author has an hindex of 4, co-authored 5 publications receiving 184 citations.
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Proceedings ArticleDOI
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories
Tiankai Tu,C. A. Rendleman,David W. Borhani,Ron O. Dror,Justin Gullingsrud,Morten Ø. Jensen,John L. Klepeis,Paul Maragakis,Patrick J. Miller,Kate A. Stafford,David E. Shaw +10 more
TL;DR: A new parallel analysis framework called HiMach, which allows users to write trajectory analysis programs sequentially, and carries out the parallel execution of the programs automatically, and an extension to the original MapReduce model to support multiple rounds of analysis.
Proceedings ArticleDOI
Anton 3: twenty microseconds of molecular dynamics simulation before lunch
David E. Shaw,Peter J. Adams,Asaph Azaria,Joseph A. Bank,Brannon Batson,Alistair Bell,Michael Bergdorf,Jhanvi Bhatt,J. Adam Butts,Timothy Correia,Robert M. Dirks,Ron O. Dror,Michael P. Eastwood,Bruce Edwards,Amos Even,Peter Feldmann,Michael Fenn,Christopher H. Fenton,Anthony Forte,Joseph Gagliardo,Gennette Gill,Maria Gorlatova,Brian Greskamp,J. P. Grossman,Justin Gullingsrud,Anissa Harper,William C. Hasenplaugh,Mark Heily,Benjamin Colin Heshmat,Jeremy Hunt,Douglas J. Ierardi,Lev Iserovich,Bryan L. Jackson,Nick P. Johnson,Mollie M. Kirk,John L. Klepeis,Jeffrey S. Kuskin,Kenneth M. Mackenzie,Roy J. Mader,Richard McGowen,Adam McLaughlin,Mark A. Moraes,Mohamed H. Nasr,Lawrence J. Nociolo,Lief O'Donnell,Andrew Parker,Jon L. Peticolas,Goran Pocina,Cristian Predescu,Terry Quan,John K. Salmon,Carl Schwink,Keun Sup Shim,Naseer Siddique,Jochen Spengler,Tamas Szalay,Raymond Tabladillo,Reinhard Tartler,Andrew G. Taube,Michael Theobald,Brian Towles,William Vick,Stanley C. Wang,Michael Wazlowski,Madeleine J. Weingarten,John M. Williams,Kevin A. Yuh +66 more
TL;DR: Anton 3 as mentioned in this paper is the fastest supercomputers in the world, achieving an order-of-magnitude improvement in time-to-solution over its predecessor, Anton 2, and is over 100 times faster than any other currently available supercomputer.
Desmond Performance on a Cluster of Multicore Processors
Edmond Chow,C. A. Rendleman,Kevin J. Bowers,Ron O. Dror,Justin Gullingsrud,Federico D. Sacerdoti,David E. Shaw +6 more
TL;DR: This report documents the performance that Desmond achieved on new hardware in April 2008, and reveals its top simulation rate is 471 ns/day on 1024 cores of an InfiniBand cluster.
Journal ArticleDOI
Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations
Willy Wriggers,Kate A. Stafford,Yibing Shan,Stefano Piana,Paul Maragakis,Kresten Lindorff-Larsen,Patrick J. Miller,Justin Gullingsrud,C. A. Rendleman,Michael P. Eastwood,Ron O. Dror,David E. Shaw +11 more
TL;DR: This paper presents automated methods for the detection of potentially important structure-changing events in long MD trajectories and provides a detailed report of broken and formed contacts that aids in the identification of specific time-dependent side-chain interactions.
Journal ArticleDOI
Computationally efficient molecular dynamics integrators with improved sampling accuracy
Cristian Predescu,Ross A. Lippert,Michael P. Eastwood,Douglas J. Ierardi,Huafeng Xu,Morten Ø. Jensen,Kevin J. Bowers,Justin Gullingsrud,C. A. Rendleman,Ron O. Dror,David E. Shaw +10 more
TL;DR: This work introduces a class of explicit variational integrators designed to achieve high accuracy for quadratic potentials, with little additional computation relative to traditional integrators, and shows that they improve accuracy for classical biomolecular simulations.