
Anton (computer) - luu
https://en.wikipedia.org/wiki/Anton_(computer)
======
HarryHirsch
There are ways to manipulate the potential surface of a system so that your
molecule of interest reaches all of available phase space within reasonable
wallclock time (read: a few days at most). The keyword is "accelerated MD";
there are several methods. The McCammon group at UCSD has done much work in
the field. This doesn't require an Anton in the basement, just a regular PC
and a modern graphics card.

The real question is: what does David Shaw, the old sphinx, propose to do with
his system? I haven't seen much research published, but the common complaint
is that he is very slow publishing.

DESRES is a weird outfit on a sunny day.

~~~
cing
You're right about enhanced sampling methods (of which aMD is just one). The
D.E. Shaw lab actually presented detailed comparisons between conventional
simulation and techniques like this at this year's Biophysical Society
Meeting. I don't see why you couldn't also run accelerated techniques on
Anton, or perhaps a related ASIC system though.

Now, you don't have to look too far to see what scientists are doing with this
system
([https://www.deshawresearch.com/publications.html](https://www.deshawresearch.com/publications.html),
[http://www.psc.edu/index.php/resources-for-
users/computing-r...](http://www.psc.edu/index.php/resources-for-
users/computing-resources/anton)). From the D.E. Shaw group alone, 7 papers in
Science, 7 papers in Nature-family journals, and 13 papers in Proc. Natl.
Acad. Sci. The publish slowly because they don't have any obligation to
publish. I can't vouch for all of those papers, but it's definitely a step in
the right direction for the field.

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cing
This page does not reference Anton 2
([http://dl.acm.org/citation.cfm?id=2683599](http://dl.acm.org/citation.cfm?id=2683599)),
there's also a really technical presentation here on the hardware if you're
into that ([http://www.hotchips.org/wp-
content/uploads/hc_archives/hc26/...](http://www.hotchips.org/wp-
content/uploads/hc_archives/hc26/HC26-11-day1-epub/HC26.11-1-High-Performance-
epub/HC26.11.130-Anton-2-Butts-Shaw-Shaw-Res-Search.pdf))

------
gamesbrainiac
When does a computer become defined as massively parallel? 100+ cores?

~~~
andrepd
Maybe it's a qualitative difference, as in parallel by design, not just
throwing a bunch of nodes together in a typical Beowulf configuration.

