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m Maintain {{WPBS}} and vital articles: 5 WikiProject templates. Merge {{VA}} into {{WPBS}}. Keep majority rating "B" in {{WPBS}}. Remove 5 same ratings as {{WPBS}} in {{WikiProject Physics}}, {{WikiProject Chemistry}}, {{WikiProject Molecular Biology}}, {{WikiProject Computing}}, {{WikiProject Systems}}.
 
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== Examples of applications ==
== Live md example available ==


I have put up a page that renders a live md simulation at 1 frame per second (DNA: CAT in Born solvent, AMBER force field and software). It may be suitable for inclusion in the external links section, since it gives an immediate look at md (if not, I think something similar should be used), moreover it has instructions and code for setting up your own simulation and web display. I expect to run dynamics on that page indefinitely, quite possibly the same molecule, because I am using the simulation as a source of noise for an artificial intelligence project that is the actual purpose of the web site. Since it's a personal project, it's not tied to grant money, so I hope it will last at least as long as I do, though with contributions I'd be willing to put it on a faster server to get smooth rendering (and/or do a bigger molecule with a GPU).
This section seems like trivia for now (perhaps it could be useful if it gave a comprehensive listing of types of simulations that people run, but until then I think that the page would be better without it).


http://phobrain.com/pr/home/mol.html
Additionally, because computers continue to get faster, listings of "very long simulations" get stale rather quickly. The simulations cited in the section following the text "The following two biophysical examples are not run-of-the-mill MD simulations" are now no longer the longest simulations or the biggest systems simulated to date. In fact, simulation studies totalling 0.5 ms are no longer particularly rare (note that this "0.5 ms simulation" noted in the article is not a single continuous simulation but the aggregated simulation time of many shorter simulations).


If wikipedia does javascript, we could embed the md on the wikipedia page itself too.
Finally, there is a danger that a section like this is simply an advertisement for a biased selection of work. <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/108.161.122.218|108.161.122.218]] ([[User talk:108.161.122.218|talk]]) 19:11, 23 September 2012 (UTC)</span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->


⚫
[[User:Phobrain|Phobrain]] ([[User talk:Phobrain|talk]]) 05:59, 6 May 2016 (UTC)
== Merge with [[Molecular dynamics]] ==
:I don't think Wikipedia supports running JavaScript within articles (although there has been talk about wanting to implement JSmol in the Chembox and Drugbox templates). The external link could be useful although I could just as easily see another editor viewing it as unnecessary. Since you have a COI I'll add it and see if it sticks. [[User:Sizeofint|Sizeofint]] ([[User talk:Sizeofint|talk]]) 06:18, 6 May 2016 (UTC)


== External links modified (February 2018) ==
The whole article is highly redundant--[[Special:Contributions/92.205.19.67|92.205.19.67]] ([[User talk:92.205.19.67|talk]]) 10:35, 12 February 2014 (UTC) <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/92.192.57.120|92.192.57.120]] ([[User talk:92.192.57.120|talk]]) </span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->


Hello fellow Wikipedians,
* It is an opportunity to improve the article, but do not to merge. These things are considerably different. <small><span class="autosigned">—&nbsp;Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:P99am|P99am]] ([[User talk:P99am|talk]] • [[Special:Contributions/P99am|contribs]]) </span></small><!-- Template:Unsigned -->
::Yep, [[User:Second Quantization|Second Quantization]] ([[User talk:Second Quantization|talk]]) 09:28, 20 February 2014 (UTC)


I have just modified one external link on [[Molecular dynamics]]. Please take a moment to review [[special:diff/823896945|my edit]]. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit [[User:Cyberpower678/FaQs#InternetArchiveBot|this simple FaQ]] for additional information. I made the following changes:
== The flow diagram below infobox is missing velocity update ==
*Added archive https://web.archive.org/web/20061014192615/http://folding.stanford.edu/papers.html to http://folding.stanford.edu/papers.html


When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
It is crucially missing v=v+a*dt. Am I right? [[User:Oceangai|Oceangai]] ([[User talk:Oceangai|talk]]) 23:45, 27 February 2014 (UTC)
:I think you are correct. [[User:Sizeofint|Sizeofint]] ([[User talk:Sizeofint|talk]]) 03:33, 21 May 2015 (UTC)


{{sourcecheck|checked=false|needhelp=}}
Yes, of course it was missing it, it was a simplified one (made by me). But instead of just removing it, please make a better one then and add it there. Just removing other people stuff without providing an improved version is not very constructive. <small class="autosigned">—&nbsp;Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/128.214.7.97|128.214.7.97]] ([[User talk:128.214.7.97|talk]]) 06:40, 11 June 2015 (UTC)</small><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->


Cheers.—[[User:InternetArchiveBot|'''<span style="color:darkgrey;font-family:monospace">InternetArchiveBot</span>''']] <span style="color:green;font-family:Rockwell">([[User talk:InternetArchiveBot|Report bug]])</span> 02:17, 4 February 2018 (UTC)
I now added a much more detailed MD algorithm schematic -- of course this is not exactly correct either, it is impossible to make an exactly correct one in a schematic. If anybody is not happy with this, don:'t remove it, but replace it with a better one. [[User:Knordlun|Knordlun]] ([[User talk:Knordlun|talk]]) 09:32, 7 July 2015 (UTC)
:Looks great! Thanks! [[User:Sizeofint|Sizeofint]] ([[User talk:Sizeofint|talk]]) 15:39, 7 July 2015 (UTC)


== Should we fix "Examples of applications" section or leave it? ==
== Mistaken summation? ==


Hi, I am of the opinion that the Examples of applications section should give a more general overview of applications rather than focusing on specifics like it seems to currently. It very heavily references primary literature, what do you think? [[User:EvilxFish|EvilxFish]] ([[User talk:EvilxFish|talk]]) 14:38, 25 April 2018 (UTC)
Unless I'm misunderstanding something...
:Milestones can still be mentioned but general overview would seem better [[User:Galobtter|Galobtter]] ([[User talk:Galobtter|pingó mió]]) 17:25, 29 April 2018 (UTC)
in the section 'Pair potentials versus many-body potentials',
in the second equation (for U sub i,j) of that section,
the first term should not have a summation, right?


== Term Atomistics ==
Sincerely,
[[User:DrTLesterThomas|DrTLesterThomas]] ([[User talk:DrTLesterThomas|talk]]) 18:43, 19 February 2015 (UTC)
:Should any of the terms have summations? If this is the potential between a pair of particles why sum over all particles? [[User:Sizeofint|Sizeofint]] ([[User talk:Sizeofint|talk]]) 03:50, 21 May 2015 (UTC)


The term "Atomistics" redirects here, but the article makes no use of the term. Are the terms "Molecular dynamics" and "Atomistics" synonymous, or should Atomistics be a topic within Molecular dynamics? I don't have enough knowledge about the field to know the best way to resolve this. Thank you. [[User:MissionInn.Jim|MissionInn.Jim]] ([[User talk:MissionInn.Jim|talk]]) 20:45, 23 November 2019 (UTC)
== Paragraph to remove ==
I propose to delete the paragraph beginning with the words "Some results of simulations ..."
This section contains some amateur discussion of protein folding problem. In spite of the serious references the text is misleading.
Article does not lose anything because this section is not about MD itself but about the specific problem.
⚫
[[User:P99am|P99am]] ([[User talk:P99am|talk]]) 09:35, 21 June 2015 (UTC)
:Agreed [[User:Sizeofint|Sizeofint]] ([[User talk:Sizeofint|talk]]) 15:43, 21 June 2015 (UTC)


== History of MD ==
*[https://en.wikipedia.org/wiki/Talk:Molecular_dynamics/Archive_1#NPOV This has been explained in a section above]. If you want to improve the description of this method limitations, that's fine - please bring more sources about this and rewrite. However, noticing limitations of the method is important per WP:NPOV. This part should not be simply removed. [[User:My very best wishes|My very best wishes]] ([[User talk:My very best wishes|talk]]) 18:34, 31 August 2015 (UTC)

*:I agree that there should be discussion of the method's limitations, but the existing text is really dated. The most recent reference in that paragraph is Levitt's 1999 paper! The preceding list of biophysics applications reads strangely, too; certainly docking shouldn't be first on the list. [[User:Opabinia regalis|Opabinia regalis]] ([[User talk:Opabinia regalis|talk]]) 22:17, 2 September 2015 (UTC)
What's about [https://en.wikisource.org/wiki/Popular_Science_Monthly/Volume_14/January_1879/Molecular_Dynamics it]? [[User:Жабыш|Жабыш]] ([[User talk:Жабыш|talk]]) 05:47, 3 December 2019 (UTC)
:::This is a complicated issue to discuss. Hence just a few points.
# I agree that text should be probably rearranged to clarify that it was about MD in general, rather than about protein folding (protein folding is simply an example that clarifies what the general problems are);
#Nothing in the underlying force fields which are currently used has ''fundamentally '' changed during this time to my knowledge, so all arguments and sources are still valid.
#If you or anyone else want to bring newer publications on the subject of MD applicability (and I know that a lot has been published), they are more than welcome. For example, someone might think that polarizable force fields helped to resolve any problems described in the "limitations" section. If so, one should simply describe: (a) what the problems are/were, and (b) how exactly they have been resolved - per sources. I can not do it because to my knowledge these problems have not been resolved. If they were resolved, we would had precise 3D models of all proteins from numerous genomes generated by energy minimization and MD. But we only have very poor quality models generated at the [http://beta.proteinmodelportal.org/ Protein Model Portal] by very old and primitive [[homology modeling]] because it works much better than "ab initio" MD. [[User:My very best wishes|My very best wishes]] ([[User talk:My very best wishes|talk]]) 01:54, 4 September 2015 (UTC)
#P.S. If [[Michael Levitt]] changed his opinion about MD, this should be noted. [[User:My very best wishes|My very best wishes]] ([[User talk:My very best wishes|talk]]) 02:14, 4 September 2015 (UTC)
:::While there haven't been any fundamental changes in the basic model, there have been significant advances in the quality of the force field parameters - as judged by e.g. comparison to NMR measurements - and in the compute resources available, as well as a correspondingly deeper appreciation of protein conformational variability on the experimental side of things. None of that stuff is a game-changer on its own but collectively the relative weights of different problems have changed quite a bit with respect to application to proteins.
:::I don't know if Levitt himself has changed his opinion about MD, but the quote highlighted in the article really does sound like old business. Overall interest in CASP has declined, Rosetta is everywhere, and model refinement isn't really a common use case, current or anticipated, for MD. The model portal and similar 'model the proteome' style projects have always been mostly grant bait, and polarizability is vaporware.
:::I started to rewrite some of this but it's too much like doing work after work ;) At least the applications sentence should really be refactored; putting docking first has to be some kind of clever troll. Docking people outside of Schrödinger can't seem to stand MD. [[User:Opabinia regalis|Opabinia regalis]] ([[User talk:Opabinia regalis|talk]]) 06:44, 4 September 2015 (UTC)
::::That's fine. But we need a "criticism" section written in a language people can understand. OK, let's say it in a different way. People who use this method tend to think that they are seeing actual/real movements of atoms. Yes, in a way they do - in a very crude approximation, and on a limited time scale. However, method fail during simulations of complex processes, such as [[protein folding]]. That has been openly admitted by a scientist who received Nobel prize for developing and applying this method to proteins. This is happening because the underlying "potential energy" functions do not directly account for a number of fundamentally important factors, such as the environment-dependence of interatomic interactions, hydrophobic interactions and conformational entropy. That's why "docking people" usually do not use MD (actually, some of them do) - exactly as you tell. That's why people are developing alternative energy functions, even such as [[statistical potential]]. [[User:My very best wishes|My very best wishes]] ([[User talk:My very best wishes|talk]]) 13:16, 4 September 2015 (UTC)
:::::I suppose I'm circuitously getting back around to your point 1, that a discussion of limitations should distinguish between the general limitations that arise due to the approximations made in modeling the underlying physics, and the issues that apply to specific use cases. Poor-quality force field parameters is an issue with a foot on either side of the fence, and if you believe any of the DE Shaw papers from a couple of years ago (e.g. PMID 22513870), is the most significant obstacle to both protein folding and model refinement (at least, if you have vast amounts of computing resources to throw at the issue). [[User:Opabinia regalis|Opabinia regalis]] ([[User talk:Opabinia regalis|talk]]) 04:31, 5 September 2015 (UTC)
::::::Yes, I think [http://www.ncbi.nlm.nih.gov/pubmed/22513870 this paper by Shaw] is worth mentioning, even though he did this in "post-diction" (not prediction/[[CASP]]) regime. The CASPs are indeed important as the only believable way to assess the computational methods, most of which are not MD. The problems/limitations are very general but they become more apparent when one deals with global energy minimization of a complex system. In this case one should be looking for the global minimum of [[Gibbs free energy]] difference (relative to the coil in aqueous solution for proteins). Some people who do MD simulations are claiming to achieve just that, ironically with coarse-grained models. Can they do something real and better than using other methods? Only CASP can answer, but for someone who understands the physics the answer is "no". [[User:My very best wishes|My very best wishes]] ([[User talk:My very best wishes|talk]]) 12:51, 5 September 2015 (UTC)
:::::::Yes, I would suggest this review: PMID 24463371 from the Shaw group also, and a benchmark of modern force fields against NMR parameters, e.g. PMID 22754404 from Pande.
:::::::From the view of a physicist, yes, the deficiencies are general and irresolvable without modifying the model. From the view of a protein biochemist, the deficiencies are relevant only to the extent that they affect the results, which for most uses are not ''ab initio'' predictions of folded globular structures. (Arguably most usage of MD by experimentalists is as a confirmation bias engine, but that's OR... ;) [[User:Opabinia regalis|Opabinia regalis]] ([[User talk:Opabinia regalis|talk]]) 05:46, 7 September 2015 (UTC)
::::::::OK. But a statement from second paper is misleading ("Although early force field development was limited by the lack of direct comparisons between simulation and experiment ..."). This is not true. The parameters of all force fields have been actually ''fitted'' to reproduce experimental data from the Day 1. The only question which exactly data. For example, one can reproduce equilibrium geometries of molecules in the crystal if interatomic distances in 6-12 potentials are right, regardless to the depths of potentials. No question that a lot of various data can be reproduced, however if method fails in practical problems, such as docking, (and the specialized "docking CASPs" did not show good performance of MD), there should be something seriously problematic with MD. 14:30, 7 September 2015 (UTC)

Latest revision as of 14:01, 10 January 2024


Live md example available

[edit]

I have put up a page that renders a live md simulation at 1 frame per second (DNA: CAT in Born solvent, AMBER force field and software). It may be suitable for inclusion in the external links section, since it gives an immediate look at md (if not, I think something similar should be used), moreover it has instructions and code for setting up your own simulation and web display. I expect to run dynamics on that page indefinitely, quite possibly the same molecule, because I am using the simulation as a source of noise for an artificial intelligence project that is the actual purpose of the web site. Since it's a personal project, it's not tied to grant money, so I hope it will last at least as long as I do, though with contributions I'd be willing to put it on a faster server to get smooth rendering (and/or do a bigger molecule with a GPU). 

 http://phobrain.com/pr/home/mol.html

If wikipedia does javascript, we could embed the md on the wikipedia page itself too.

Phobrain (talk) 05:59, 6 May 2016 (UTC)[reply]

I don't think Wikipedia supports running JavaScript within articles (although there has been talk about wanting to implement JSmol in the Chembox and Drugbox templates). The external link could be useful although I could just as easily see another editor viewing it as unnecessary. Since you have a COI I'll add it and see if it sticks. Sizeofint (talk) 06:18, 6 May 2016 (UTC)[reply]
[edit]

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Should we fix "Examples of applications" section or leave it?

[edit]

Hi, I am of the opinion that the Examples of applications section should give a more general overview of applications rather than focusing on specifics like it seems to currently. It very heavily references primary literature, what do you think? EvilxFish (talk) 14:38, 25 April 2018 (UTC)[reply]

Milestones can still be mentioned but general overview would seem better Galobtter (pingó mió) 17:25, 29 April 2018 (UTC)[reply]

Term Atomistics

[edit]

The term "Atomistics" redirects here, but the article makes no use of the term. Are the terms "Molecular dynamics" and "Atomistics" synonymous, or should Atomistics be a topic within Molecular dynamics? I don't have enough knowledge about the field to know the best way to resolve this. Thank you. MissionInn.Jim (talk) 20:45, 23 November 2019 (UTC)[reply]

History of MD

[edit]

What's about it? Жабыш (talk) 05:47, 3 December 2019 (UTC)[reply]

Retrieved from "https://en.wikipedia.org/enwiki/w/index.php?title=Talk:Molecular_dynamics&oldid=1194737939"