Proceedings ArticleDOI
Millisecond-scale molecular dynamics simulations on Anton
David E. Shaw,Ron O. Dror,John K. Salmon,J. P. Grossman,Kenneth M. Mackenzie,Joseph A. Bank,Cliff Young,Martin M. Deneroff,Brannon Batson,Kevin J. Bowers,Edmond Chow,Michael P. Eastwood,Douglas J. Ierardi,John L. Klepeis,Jeffrey S. Kuskin,Richard H. Larson,Kresten Lindorff-Larsen,Paul Maragakis,Mark A. Moraes,Stefano Piana,Yibing Shan,Brian Towles +21 more
- pp 39
TLDR
Anton's performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations is reported, allowing the observation of aspects of protein dynamics that were previously inaccessible to both computational and experimental study.Abstract:
Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first time the simulation of biological molecules at an atomic level of detail for periods on the order of a millisecond---about two orders of magnitude beyond the previous state of the art. Anton is now running simulations on a timescale at which many critically important, but poorly understood phenomena are known to occur, allowing the observation of aspects of protein dynamics that were previously inaccessible to both computational and experimental study. Here, we report Anton's performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations. We also discuss the manner in which novel algorithms have been coordinated with Anton's co-designed, application-specific hardware to achieve these results.read more
Citations
More filters
Journal ArticleDOI
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen,Stefano Piana,Kim Palmo,Paul Maragakis,John L. Klepeis,Ron O. Dror,David E. Shaw,David E. Shaw +7 more
TL;DR: A new force field, which is termed Amber ff99SB‐ILDN, exhibits considerably better agreement with the NMR data and is validated against a large set of experimental NMR measurements that directly probe side‐chain conformations.
Journal ArticleDOI
How Fast-Folding Proteins Fold
TL;DR: Results of atomic-level molecular dynamics simulations of 12 proteins reveal a set of common principles underlying the folding of 12 structurally diverse proteins that spontaneously and repeatedly fold to their experimentally determined native structures.
Journal ArticleDOI
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw,David E. Shaw,Paul Maragakis,Kresten Lindorff-Larsen,Stefano Piana,Ron O. Dror,Michael P. Eastwood,Joseph A. Bank,John M. Jumper,John K. Salmon,Yibing Shan,Willy Wriggers +11 more
TL;DR: Simulation of the folding of a WW domain showed a well-defined folding pathway and simulation of the dynamics of bovine pancreatic trypsin inhibitor showed interconversion between distinct conformational states.
Journal ArticleDOI
Biomolecular Simulation: A Computational Microscope for Molecular Biology
TL;DR: The rapidly evolving state of the art for atomic-level biomolecular simulation is described, the types of biological discoveries that can now be made through simulation are illustrated, and challenges motivating continued innovation in this field are discussed.
Journal ArticleDOI
How robust are protein folding simulations with respect to force field parameterization
TL;DR: It is found that although it is important to match a single, experimentally determined structure and folding rate, this does not ensure that a given simulation will provide a unique and correct description of the full free-energy surface and the mechanism of folding.
References
More filters
Journal ArticleDOI
A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Journal ArticleDOI
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.
Journal ArticleDOI
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
TL;DR: In this article, the parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described, and the parameters for both torsional and non-bonded energy properties have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER force field.
Book
Computer simulation using particles
R W Hockney,J W Eastwood +1 more
TL;DR: In this paper, a simulation program for particle-mesh force calculation is presented, based on a one-dimensional plasma model and a collisionless particle model, which is used to simulate collisionless particle models.
Journal ArticleDOI
Comparison of multiple Amber force fields and development of improved protein backbone parameters.
Viktor Hornak,Robert Abel,Asim Okur,Bentley Strockbine,Adrian E. Roitberg,Carlos Simmerling,Carlos Simmerling +6 more
TL;DR: An effort to improve the φ/ψ dihedral terms in the ff99 energy function achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data.
Related Papers (5)
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell,D. Bashford,M. Bellott,Roland L. Dunbrack,Jeffrey D. Evanseck,Martin J. Field,Stefan Fischer,Jiali Gao,H. Guo,S. Ha,Diane Joseph-McCarthy,L. Kuchnir,K. Kuczera,F. T. K. Lau,C. Mattos,Stephen W. Michnick,Thien H. Ngo,D. T. Nguyen,B. Prodhom,W. E. Reiher,Benoît Roux,M. Schlenkrich,Jeremy C. Smith,Roland H. Stote,John E. Straub,Masakatsu Watanabe,J. Wiórkiewicz-Kuczera,D. Yin,Martin Karplus +28 more