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This material was placed on main page, but doesn't really fit there as written (it is argumentative in tone, and a digression from this topic). But there may be useful material to use on some "comparison of MD systems" article and/or in the Folding@home article:
{{
cite web}}
: Check date values in: |date=
(
help)
Note: It appears that Folding@home achieves millisecond timescales by performing large ensembles of of relatively short trajectories as a means of sampling the space (as opposed to Anton's single long trajectories). Moreover, Folding@home uses an implicit solvent model which is computationally simpler than an explicit solvent. Both projects certainly have scientific value, but the timescales mentioned are not directly comparable from either a computational or chemical perspective. LotLE× talk 02:03, 21 September 2011 (UTC)
Claiming that Folding@Home is equivalent in performance to Anton because they both have run the same aggregate chemical time is like saying that the Ford Taurus is equivalent to the Space Shuttle because they've both traveled the same number of aggregate miles. Anton can run a single trajectory very fast, which is quite useful for finding pathways between states. Highly parallel statistical things like Folding@Home can do some high throughput exploration of the energy landscape around some known state--it is of limited utility in identifying pathways. They are both useful tools. Also, the comparison of aggregate chemical time is flawed because I believe you are comparing all of Folding@Home's chemical time against one hero run on one Anton machine taking on the order of a couple months. There are *many* Anton machines which have been running for at least a couple years now.
Regardless, why is there all this discussion of Folding@Home on the Anton page? Should I head over to the Folding@Home page and litter it with comparisons to Anton? — Preceding unsigned comment added by 74.73.228.91 ( talk) 04:46, 20 October 2011 (UTC)
I would like to issue a general apology to all parties that I may have offended with the non-neutral content. It was wrong of me to place this content in the way that it was worded on the Anton page. This has been pointed out to me, both by Wikipedians and anonymous IPs. I should not have made a comparison between Anton and F@h without looking at both sides of the issue. On the
Folding@home page, the neutrality of the
comparison to Anton was recently
called into question which I have addressed. My research for this fix has involved reading of both F@h and Anton publications, from which I have since learned how powerful and useful Anton really is. In light of this discovery, I realize now that it was definitely not appropriate for that biased comparison to be in the page. I thus detract it. Anton and F@h should be compared in a neutral way, with facts backed up by scientific publications instead of blogs and forum posts. Such comparisons should not "cast a shadow" over Anton, for it is a very useful tool which like F@h will continue to provide unique insights into the complexities of protein folding. Humbled,
Jessemv (
talk) 02:24, 9 November 2011 (UTC)
While I don't disagree that is is interesting to see how F@h and Anton differ in their approaches to computation and aggregate ensembles, this addition basically turns this article on Anton into one about Folding@home, which is really WP:UNDUE, and generally off-topic. I put the material here on the talk page, but it really needs a home somewhere different to be appropriate. LotLE× talk 00:37, 28 October 2011 (UTC)
Jessmv: I think what would be more useful that losing focus within this article would be to have a general article called Comparison of molecular dynamics systems that could encompass Folding@Home, Anton, and other software (or hardware) systems as well. This could allow for comparisons of a variety of dimensions, and I think the existing articles and categories provide some guidance. For example:
I'm sure there are other dimensions too, but those are a few that occur to me. It might make sense to present much of this comparison in one or more columns, although citations are obviously important, and incorporating more descriptive text within the envisioned article would help also. LotLE× talk 01:29, 28 October 2011 (UTC)
References
{{
cite journal}}
: CS1 maint: multiple names: authors list (
link)
So I've read through most of the references and some of the paywalled ones, and nowhere did I see an answer to these questions: how much does an Anton cost to build, and then how much does it cost to run? I can make guesses at both based on ASIC costs and power consumption, but I'd rather not. Does anyone know? -- Gwern (contribs) 01:35 20 April 2012 (GMT)
Anyone who is interested in expanding this article might be interested in the paper "Anton, a special-purpose machine for molecular dynamics simulation", written in 2007. this might be a publicly-working link to a PDF. • Jesse V. (talk) 14:36, 15 September 2012 (UTC)
how to download trajectories computed by anton? I saw many articles said they download the trajectories, but i can't find the link to the trajectories on the publication page. — Preceding unsigned comment added by 108.236.198.181 ( talk) 03:19, 21 May 2013 (UTC)
It says right there that "Folding@home has achieved aggregate ensemble simulation timescales similar to those Anton has, specifically achieving the 1.5 millisecond range in January 2010". This is incorrect because 1,5 millisecond is not similar to 17.000 nanoseconds = 17 microseconds. 1,5 milliseconds is 3 orders of magnitude ( 1000 times ) bigger than 17 microseconds ( 17.000 nanoseconds ).
I'd like to pull Unforgettableid in to this discussion in particular, since he's raised concerns about notability and autobiography. The involvement of Anxdo is a fair point, but it's also unclear how to address the concerns raised by your flag. The content itself is largely neutral and focused on factual details, and my understanding is that's ultimately what matters. Are there specific passages you're concerned about?
As far as notability, the point about sources is fair (although I've seen worse and these are reputable journals), but it strikes me as more of a "needs citations for verification" situation than a general notability one.
On a related note, perhaps Anton (computer) should be merged into D. E. Shaw Research, as the notability of the two are tied to each other. That could also make NPOV sourcing easier to address. Desmond (software) should probably stay separate as it's more widely used. Proxyma ( talk) 04:37, 22 November 2013 (UTC)
Disagree about merging Anton (computer) and DEShawRes. There is one Anton with nominally public access so there is some validity is seperating them (as in parent/child) cowburn —Preceding undated comment added 21:55, 2 November 2015 (UTC)
The Link to the pdf given here [1] is incorrect. It should refer to the Anton 2 paper refered to by the DOI 10.1109/SC.2014.9 but the pdf seems to be describing Anton 1 and has different authors. I am removing the direct link to the pdf. — Preceding unsigned comment added by Lpd-Lbr ( talk • contribs) 10:53, 9 May 2019 (UTC)
References
{{
cite book}}
: |journal=
ignored (
help)
This topic now seems sufficiently neutral and non-partisan. It contains interesting information about the device. I will remove the warning in a few days if there are no objections. — Preceding unsigned comment added by Cowburn ( talk • contribs) 14:10, 13 August 2020 (UTC)
DE Shaw has a talk in the upcoming Hot Chips conference, concerning the 3rd version of their ASIC. The talk is listed in the advance program summary on the conference website, no login required. For now there is only a title with authors.
Hot Chips 2021 - August 22-24, 2021 [1]
- On-Line - A symposium on High-Performance Chips
- (Conference day 2, 11:30)
The Anton 3 ASIC: a Fire-Breathing Monster for Molecular Dynamics Simulations, J. Adam Butts and David E. Shaw, D.E. Shaw Research
Robert Munafo ( talk) 14:55, 14 May 2021 (UTC)
References
Anton 3 has been placed in service since this article last received content updates. [1] The newest version apparently shows significant capacity upgrades and the article is likely due for an update. 2603:6011:5B02:3CE6:A52B:D954:D18D:E3B1 ( talk) 01:29, 2 August 2023 (UTC)
This article is rated Start-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | |||||||||||
|
The following Wikipedia contributor has declared a personal or professional connection to the subject of this article. Relevant policies and guidelines may include
conflict of interest,
autobiography, and
neutral point of view.
|
This material was placed on main page, but doesn't really fit there as written (it is argumentative in tone, and a digression from this topic). But there may be useful material to use on some "comparison of MD systems" article and/or in the Folding@home article:
{{
cite web}}
: Check date values in: |date=
(
help)
Note: It appears that Folding@home achieves millisecond timescales by performing large ensembles of of relatively short trajectories as a means of sampling the space (as opposed to Anton's single long trajectories). Moreover, Folding@home uses an implicit solvent model which is computationally simpler than an explicit solvent. Both projects certainly have scientific value, but the timescales mentioned are not directly comparable from either a computational or chemical perspective. LotLE× talk 02:03, 21 September 2011 (UTC)
Claiming that Folding@Home is equivalent in performance to Anton because they both have run the same aggregate chemical time is like saying that the Ford Taurus is equivalent to the Space Shuttle because they've both traveled the same number of aggregate miles. Anton can run a single trajectory very fast, which is quite useful for finding pathways between states. Highly parallel statistical things like Folding@Home can do some high throughput exploration of the energy landscape around some known state--it is of limited utility in identifying pathways. They are both useful tools. Also, the comparison of aggregate chemical time is flawed because I believe you are comparing all of Folding@Home's chemical time against one hero run on one Anton machine taking on the order of a couple months. There are *many* Anton machines which have been running for at least a couple years now.
Regardless, why is there all this discussion of Folding@Home on the Anton page? Should I head over to the Folding@Home page and litter it with comparisons to Anton? — Preceding unsigned comment added by 74.73.228.91 ( talk) 04:46, 20 October 2011 (UTC)
I would like to issue a general apology to all parties that I may have offended with the non-neutral content. It was wrong of me to place this content in the way that it was worded on the Anton page. This has been pointed out to me, both by Wikipedians and anonymous IPs. I should not have made a comparison between Anton and F@h without looking at both sides of the issue. On the
Folding@home page, the neutrality of the
comparison to Anton was recently
called into question which I have addressed. My research for this fix has involved reading of both F@h and Anton publications, from which I have since learned how powerful and useful Anton really is. In light of this discovery, I realize now that it was definitely not appropriate for that biased comparison to be in the page. I thus detract it. Anton and F@h should be compared in a neutral way, with facts backed up by scientific publications instead of blogs and forum posts. Such comparisons should not "cast a shadow" over Anton, for it is a very useful tool which like F@h will continue to provide unique insights into the complexities of protein folding. Humbled,
Jessemv (
talk) 02:24, 9 November 2011 (UTC)
While I don't disagree that is is interesting to see how F@h and Anton differ in their approaches to computation and aggregate ensembles, this addition basically turns this article on Anton into one about Folding@home, which is really WP:UNDUE, and generally off-topic. I put the material here on the talk page, but it really needs a home somewhere different to be appropriate. LotLE× talk 00:37, 28 October 2011 (UTC)
Jessmv: I think what would be more useful that losing focus within this article would be to have a general article called Comparison of molecular dynamics systems that could encompass Folding@Home, Anton, and other software (or hardware) systems as well. This could allow for comparisons of a variety of dimensions, and I think the existing articles and categories provide some guidance. For example:
I'm sure there are other dimensions too, but those are a few that occur to me. It might make sense to present much of this comparison in one or more columns, although citations are obviously important, and incorporating more descriptive text within the envisioned article would help also. LotLE× talk 01:29, 28 October 2011 (UTC)
References
{{
cite journal}}
: CS1 maint: multiple names: authors list (
link)
So I've read through most of the references and some of the paywalled ones, and nowhere did I see an answer to these questions: how much does an Anton cost to build, and then how much does it cost to run? I can make guesses at both based on ASIC costs and power consumption, but I'd rather not. Does anyone know? -- Gwern (contribs) 01:35 20 April 2012 (GMT)
Anyone who is interested in expanding this article might be interested in the paper "Anton, a special-purpose machine for molecular dynamics simulation", written in 2007. this might be a publicly-working link to a PDF. • Jesse V. (talk) 14:36, 15 September 2012 (UTC)
how to download trajectories computed by anton? I saw many articles said they download the trajectories, but i can't find the link to the trajectories on the publication page. — Preceding unsigned comment added by 108.236.198.181 ( talk) 03:19, 21 May 2013 (UTC)
It says right there that "Folding@home has achieved aggregate ensemble simulation timescales similar to those Anton has, specifically achieving the 1.5 millisecond range in January 2010". This is incorrect because 1,5 millisecond is not similar to 17.000 nanoseconds = 17 microseconds. 1,5 milliseconds is 3 orders of magnitude ( 1000 times ) bigger than 17 microseconds ( 17.000 nanoseconds ).
I'd like to pull Unforgettableid in to this discussion in particular, since he's raised concerns about notability and autobiography. The involvement of Anxdo is a fair point, but it's also unclear how to address the concerns raised by your flag. The content itself is largely neutral and focused on factual details, and my understanding is that's ultimately what matters. Are there specific passages you're concerned about?
As far as notability, the point about sources is fair (although I've seen worse and these are reputable journals), but it strikes me as more of a "needs citations for verification" situation than a general notability one.
On a related note, perhaps Anton (computer) should be merged into D. E. Shaw Research, as the notability of the two are tied to each other. That could also make NPOV sourcing easier to address. Desmond (software) should probably stay separate as it's more widely used. Proxyma ( talk) 04:37, 22 November 2013 (UTC)
Disagree about merging Anton (computer) and DEShawRes. There is one Anton with nominally public access so there is some validity is seperating them (as in parent/child) cowburn —Preceding undated comment added 21:55, 2 November 2015 (UTC)
The Link to the pdf given here [1] is incorrect. It should refer to the Anton 2 paper refered to by the DOI 10.1109/SC.2014.9 but the pdf seems to be describing Anton 1 and has different authors. I am removing the direct link to the pdf. — Preceding unsigned comment added by Lpd-Lbr ( talk • contribs) 10:53, 9 May 2019 (UTC)
References
{{
cite book}}
: |journal=
ignored (
help)
This topic now seems sufficiently neutral and non-partisan. It contains interesting information about the device. I will remove the warning in a few days if there are no objections. — Preceding unsigned comment added by Cowburn ( talk • contribs) 14:10, 13 August 2020 (UTC)
DE Shaw has a talk in the upcoming Hot Chips conference, concerning the 3rd version of their ASIC. The talk is listed in the advance program summary on the conference website, no login required. For now there is only a title with authors.
Hot Chips 2021 - August 22-24, 2021 [1]
- On-Line - A symposium on High-Performance Chips
- (Conference day 2, 11:30)
The Anton 3 ASIC: a Fire-Breathing Monster for Molecular Dynamics Simulations, J. Adam Butts and David E. Shaw, D.E. Shaw Research
Robert Munafo ( talk) 14:55, 14 May 2021 (UTC)
References
Anton 3 has been placed in service since this article last received content updates. [1] The newest version apparently shows significant capacity upgrades and the article is likely due for an update. 2603:6011:5B02:3CE6:A52B:D954:D18D:E3B1 ( talk) 01:29, 2 August 2023 (UTC)