Anton

Anton is a special purpose supercomputer for biomolecular simulation designed and constructed by D. E. Shaw Research (DESRES).   PSC’s current system is known as Anton 2 and is a successor to the original Anton 1 machine hosted here.

Anton 2, the next-generation Anton supercomputer, is a 128 node system, made available without cost by DESRES for non-commercial research use by US universities and other not-for-profit institutions, and is hosted by PSC with support from the NIH National Institute of General Medical Sciences.  It replaced the original Anton 1 system in the fall of 2016.

Anton was designed to dramatically increase the speed of molecular dynamics (MD) simulations compared with the previous state of the art, allowing biomedical researchers to understand the motions and interactions of proteins and other biologically important molecules over much longer time periods than was previously accessible to computational study.  The MD research community is using the Anton 2 machine at PSC to investigate important biological phenomena that due to their intrinsically long time scales have been outside the reach of even the most powerful general-purpose scientific computers.  Application areas include biomolecular energy transformation, ion channel selectivity and gating, drug interactions with proteins and nucleic acids, protein folding and protein-membrane signaling.

See the press release announcing that Anton 2 was coming to PSC.

Apply

Anton 2 is allocated annually via a Request for Proposal with proposals reviewed by a committee convened by the National Research Council at the National Academies. To qualify for an allocation on Anton 2, the principal investigator must be a faculty or staff member at a U.S. academic or non-profit research institution.

Applications are being accepted now.  The application deadline is Thursday, June 23. 

• See the RFP

Anton workshop

A workshop is offered each fall covering all aspects of running MD simulations on Anton 2.  It is by invitation only for those who received an allocations award in the most recent opportunity. See more about the workshop.

Getting Started on Anton 2

We keep all Anton 2 documentation and instructions at the Anton wiki at https://wiki.psc.edu/twiki/viewauth/Anton/WebHome

This wiki can be accessed with your PSC username/password combo. If you forget your password, you can reset it at  apr.psc.edu.

The preferred way of communicating with PSC support staff and with other users who share their experiences is through the Anton forum on the wiki. Please sign up at: https://wiki.psc.edu/twiki/view/Anton/AntonForum

After signing up, if you experience problems or difficulties, please check the Anton Forum section of the Wiki to make sure your problem has not been addressed before. There is a text file to make it easier to search, and sections for Frequently Asked Questions and Troubleshooting Tips. If your problem is not there, please feel free to email anton-forum@psc.edu for help. 

Accounts for running on Anton 2 and for participating in the workshop cannot be created until the PIs and the group members have sent a signed End User Agreement, as explained below.

Anton End User Agreement

All users who are awarded time on Anton2  must complete the Anton End User Agreement (EUA) acknowledging that they have read and understood their responsibilities as an Anton 2 user and agree to comply.  Once it is signed, return the EUA to grants@psc.edu.

Get the EUA

Acknowledgement in publications

Project summaries

See project summaries for some Anton 1 research..

Research highlights

Here are highlights of just some of the groundbreaking research enabled by Anton:

Molecular mechanisms of arrestin activation – Simulations provide a structural foundation for the design of functionally selective ligands that lead to particular GPCR signaling profiles. N. Latorraca and R. Dror. doi:10.1038/s41586-018-0077-3

Uncovering new ways to target flu viruses – A conserved amino acid could provide a target toward a universal vaccine for viruses. Xingcheng Lin, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma, and Jose Onuchic. doi:10.1073/pnas.1805442115.

Kink formation is required for lateral gating in BamA – Simulations of BamA reveal a dynamic gating between the N- and C-terminal strands at the barrel seam. Using free-energy calculations and mutagenesis experiments, it was determined that the C-terminus has to kink inward for efficient opening. lateral gating in BamA. Karl Lundquist, Jeremy Bakelar, Nicholas Noinaj, and JC Gumbart. doi:10.1073/pnas.1722530115

World’s Tiniest Test Tubes in Alzheimer’s Protein Simulation – Simulations of plaque-forming beta amyloid molecules offer insights towards possible Alzheimer’s drug therapies. From PSC’s Science Highlights Fall 2018. G. Eskici and P.H. Axelsen. doi:10.1021/acs.langmuir.7b04192.

“Sticky and Loose Ends” Shed Light on Heart Health – Simulations show APOA1 protein ends link to hold together “the good cholesterol”. From PSC’s Science Highlights Fall 2018. Mohsen Pourmousa, Richard Pastor, Jere Segrest, et. al. doi: 10.1073/pnas.1721181115

Locked, Not Loaded – New target in HIV-1 replication. Simulations may lead to more effective anti-maturation drugs to fight AIDS and possibly other viral diseases. From PSC’s Science Highlights Spring 2018. J. Perilla et al. doi:10.1038/s41467-017-01856-y.

Snapping into Place – Simulations give clue to poorly understood role of tubulin, the cell’s “Lego bricks”.   From PSC’s Science Highlights Spring 2018. David Hoogerheide. doi:10.1073/pnas.1721181115.

Inner Space – Work on Anton highlights the importance of empty space for protein function. Simulations of T4 lysozyme L99A show that big gaps opened up in the protein, which “let in” molecules roughly the size of drug molecules. From PSC’s Science Highlights Fall 2017.

Hooked Up – Simulations on Anton discover the critical role disulfides play in holding together MCoTI-II, a natural pesticide that would fall apart without disulfide bridges. From PSC’s Science Highlights Spring 2017.

“The Dynamics of Single Protein Molecules Is Non-Equilibrium and Self-Similar over Thirteen Decades in Time.”  Nature Physics 12, no. 2 (2016): 171–74. doi:10.1038/nphys3553.  Hu, Xiaohu, Liang Hong, Micholas Dean Smith, Thomas Neusius, Xiaolin Cheng, and Jeremy C. Smith. This article was highlighted in the cover of Nature Physics and discussed in the following article: Metzler R, News and Views Protein physics: Forever ageing, Nature Phys., 2016, 12, 113–114, doi:10.1038/nphys3585.

“Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide”. Biophysical Journal 110, no. 8 (April 2016): 1744–52. doi:10.1016/j.bpj.2016.03.027.  Zhang, Yi, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson, and Norelle L. Daly. This article was featured on the cover of the Biophysical Journal.

Island time: “Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin.” Biophysical Journal 109, no. 5 (September 2015): 948–55. doi:10.1016/j.bpj.2015.07.036  Sodt, Alexander J., Richard W. Pastor, and Edward Lyman. This study was featured on the cover of the Biophysical Journal and highlighted as New and Notable: http://www.cell.com/biophysj/abstract/S0006-3495(15)00772-9

Janus Channel – Anton simulations reveal how pain, epilepsy drugs work through same target protein, from PSC’s Projects in Scientific Computing, Spring 2015.

A TUG Felt Elsewhere – Anton simulations show how drug-producing enzyme is enhanced by changes far from reactive site, from PSC’s Projects in Scientific Computing, Fall 2014.

Roll Out the Beta Barrels – Anton simulations reveal how dangerous bacteria install critical proteins, from PSC’s Projects in Scientific Computing, Spring 2014.

Two Steps Forward, One Step Back – molecular dynamics simulations disclose how water leaving and then re-entering the potassium channel delays its return to the active state, from PSC’s Projects in Scientific Computing, Spring 2014.

A Movie is Worth a Million Pictures – structural dynamics simulations illuminate the mechanisms of sodium-coupled substrate binding/release in an aspartate transporter, from PSC’s 2013 annual report, Projects in Scientific Computing

Epic Microseconds – four projects yielding invaluable insights into the structure and function of proteins from PSC’s 2012 annual report, Projects in Scientific Computing

Protein Research Leaps Forward – four projects in MD simulation from PSC’s 2011 annual report, Projects in Scientific Computing

Atomic-Level Characterization of the Structural Dynamics of Proteins – This paper, published in Science, details the first millisecond MD simulation on Anton.
Shaw, David E., 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. “Atomic-Level Characterization of the Structural Dynamics of Proteins” Science 15 Oct 2010: 341-346 DOI: 10.1126/science.1187409

Millisecond-scale molecular dynamics simulations on Anton – This paper (Gordon Bell prize winner for best paper at SC09 ) contains measurements of energy conservation on Anton that you can use to compare with your own simulations.