Talk:Comparison of software for molecular mechanics modeling: Difference between revisions

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{{WikiProject Physics|importance=low}}

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==Adding OpenMM==

OpenMM is quite popular and from my perspective may take AMBER's place soon. However, I don't know enough about its features to add it myself. --[[User:BobHelmut|h]] ([[User talk:BobHelmut|talk]]) 16:51, 5 July 2023 (UTC)

==Questions==

1) what is the difference between "Yes, has QM/MM" (Y) and "has QM/MM Interface" (I)? I do not know which is more developed, Y or I. Is it that Y has the capability to perform QM/MM and I has the capability as well as a user interface to facilitate model building? <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/129.186.148.15|129.186.148.15]] ([[User talk:129.186.148.15|talk]]) 14:00, 17 September 2010 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot-->

2) "DL_POLY" software, which is quite popular, is missing. <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/93.180.12.98|93.180.12.98]] ([[User talk:93.180.12.98|talk]]) 10:50, 19 June 2012 (UTC)</span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->

==Reference sections==

Would it not be a good idea to add some references, e.g. for the algorithm details, e.g. for comparing force-fields, homology model algorithms, and semiempiric details?

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* [http://www.chim.unifi.it/orac/ ORAC] (classical)

* [[XMD]] (classical)

== external links in the body of articles ==

See:

:"''External links should not normally be used in the body of an article. Instead, include appropriate external links in an 'External links' section at the end and/or in the appropriate ___location within an infobox or navbox.''" [[Wikipedia:External links#Important points to remember]]

and

:"''If an article has external links, the standard format is to place them in a bulleted list under a primary heading at the end of the article. External links should identify the link and briefly summarize the website's contents and why the website is relevant to the article.''" [[Wikipedia:External links#External links section]]

also [[WP:NOTLINK]], articles are not lists of external links.

P.D.: I was going to ask in the talk page of WP:EL, although I see that someone made already a similar question ;[[Wikipedia talk:External links/Archive 23#when are external links allowed in the body of the article?]] --[[User:Enric Naval|Enric Naval]] ([[User talk:Enric Naval|talk]]) 00:27, 3 April 2009 (UTC)

*These "policies" are only suggestions, not hard rules. The guideline, "No page should be linked from a Wikipedia article unless its inclusion is justifiable", is clear and this case is "justifiable". There are cases where it is appropriate to use external links inline (e.g., in a table). This article is certainly such a case. Until we write each of the associated articles, the external links should stay, as they ''help'' the user find the packages. This is the '''primary''' goal of Wikipedia: Helping users find the information they require. --[[User:Thorwald|Thorwald]] ([[User talk:Thorwald#top|talk]]) 00:43, 3 April 2009 (UTC)

::No, helping people to find stuff that is outside of wikipedia is a violation of [[WP:NOTDIRECTORY]]. The main goal is writing an encyclopedia ([[WP:ENC]]). Also, if you look at [[WP:REDLINK]], leaving red links compels people to write those articles. Also, people might link at the "What links here" to see if a certain mane is being used often, or to find other articles pointing at the article they are creating so they can check them out, or to check if it's linked from many articles before nominating it for deletion as a measure of its "popularity". By using external links you are breaking all of that.

::Leaving an external link will also not let you see when an article has been finally written. For example, I left a lot of wrong bluelinks like [[Desmond]], which I should have changed to [[Desmond (software)]]. However, I also made visible a few correct bluelinks: [[LAMMPS]], [[Materials Studio]], [[RasMol]], which are now replaced by external links. --[[User:Enric Naval|Enric Naval]] ([[User talk:Enric Naval|talk]]) 01:47, 3 April 2009 (UTC)

:::As I said before, these are guidelines, not rules. I don't care if it is a "violation" or not the goal of ''some'' people on Wikipedia to help people find stuff; it is ''my'' goal (and has been for the ~six years I have been active on Wikipedia). Anyway, my compromise can be seen on my last edit of the article (i.e., I moved the external links to a separate column). --[[User:Thorwald|Thorwald]] ([[User talk:Thorwald#top|talk]]) 02:06, 3 April 2009 (UTC)

::::Thank you very much. That looks good enough to me, I was mostly interested in that the names were red links; I explained my reasons [[User_talk:P99am#external links in body of articles|here]] to another editor (I reached a similar agreement with him about the links at [[List of nucleic acid simulation software]] but your version looks much better, I'll tell him about it). Again, thanks for understanding and for finding such a good solution. --[[User:Enric Naval|Enric Naval]] ([[User talk:Enric Naval|talk]]) 02:25, 3 April 2009 (UTC)

I think the original version was better, but a separate column is also acceptable. But in this case column "Website" should not contain a "link", but a source name. And should not be empty cells, even where article on Wikipedia exist. Please look at my latest version of [[List of nucleic acid simulation software]]. ([[User:P99am|P99am]] ([[User talk:P99am|talk]]) 09:00, 3 April 2009 (UTC))

Perhaps the idea of a separate column is good enough if the work is done accurately.

Look what happened now:

* We have a column with the same "link" statements.

* Some of the blue links become incorrect.

* Some names of programs black and some red, without any principle.

* Half of the links had become red. This is too much. We must keep in mind that Wikipedia for the first time for users, and only secondarily is invitetion for the editors.

To meet some formal rules are not sufficient reason to do such things. Those who want to improve the article should make a good job, but do not break the page. I therefore propose to revert to the original version - with external links. ([[User:P99am|P99am]] ([[User talk:P99am|talk]]) 14:28, 3 April 2009 (UTC))

:It is easy to criticize, but better to help fix things. You didn't give any specific examples to the new "problems" you find with my latest edit. What did you mean by "We have a column with the same 'link' statements"? Which of the blue links became "incorrect"? I fixed the names in black (you could have as well). We should rename the "links" to the names of the institutes the packages originated (like you did in [[List of nucleic acid simulation software]]). I actually now think the new version is better, as it retains the external links (for our users) and reminds the editors which articles need to be created (the red links). The new version should stay, but be improved. --[[User:Thorwald|Thorwald]] ([[User talk:Thorwald#top|talk]]) 21:02, 3 April 2009 (UTC)

::I fixed a few incorrect blue links at [[List of software for molecular mechanics modeling]]. --[[User:Enric Naval|Enric Naval]] ([[User talk:Enric Naval|talk]]) 21:31, 3 April 2009 (UTC)

::: I fixed what I knew.([[User:P99am|P99am]] ([[User talk:P99am|talk]]) 16:11, 4 April 2009 (UTC))

== Link texts and download link ==

Dear all, reading through the article I noticed several links, which only had numbers which never reappeared. I took the liberty to change those to human readable text. Similarly, some only read as "link". Is it desirable to change that text to either the ___domain of the link or the name of the software?

Also, there is one singular link to a download page of a software. Personally, I am inclined to remove this link from Wikipedia, but I am not sure whether there is a policy to follow? Thank you for any input. [[User:Kadhgar|Kadhgar]] ([[User talk:Kadhgar|talk]]) 21:31, 29 July 2011 (UTC)

== Proposal to separate simulation software from visualization-only software ==

This list contains a mixture of visualization software, like Chemitorium, and simulation-only programs like Desmond. The large number of narrow columns and the many rows in the table make it difficult to read. I propose that we break this table into two separate tables (possibly on two separate pages), one for simulation programs and one for visualization. There will be some duplication, since some packages have both capabilities....maybe three tables? This would also eliminate the "View 3D" and "Model builder" columns from each table. [[User:Oanjao|Oanjao]] ([[User talk:Oanjao|talk]]) 19:32, 25 January 2012 (UTC)

: There is a page [[List of molecular graphics systems]]. Visualization only software should not be here at all. I'm just tired to remove it. [[User:P99am|P99am]] ([[User talk:P99am|talk]]) 13:17, 26 January 2012 (UTC)

== Adding JMol ==

I think that [http://jmol.sourceforge.net/index.en.html JMol] deserves a place in this list, because it is commonly used.

[[User:Divof|Divof]] ([[User talk:Divof|talk]]) 16:59, 18 April 2014 (UTC)

== coulours ==

this list should be coloredspecially the license column <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/130.192.116.220|130.192.116.220]] ([[User talk:130.192.116.220|talk]]) 16:07, 8 July 2014 (UTC)</span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->

== GPIUTMD ==

Hi all,

I propose to delete the '''GPIUTMD'''. It seems to me that this is not the famous software. [[User:P99am|P99am]] ([[User talk:P99am|talk]]) 11:28, 12 November 2014 (UTC)

== External links modified ==

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*Added archive https://web.archive.org/web/20101010131115/http://www.biomolecular-modeling.com:80/Abalone/ to http://www.biomolecular-modeling.com/Abalone/

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== External links modified ==

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== Notable software packages ==

As the list is only for notable software, I will soon start cleaning out the list. All software without an own article will then be removed, as deemed non-notable. <span style="border:1px solid green; padding:0 2px">[[User:The Banner|<span style="color:green">The&nbsp;Banner</span>]]&nbsp;[[User talk:The Banner|<i style="color:maroon">talk</i>]]</span> 07:32, 19 September 2019 (UTC)

== Please add HOOMD-blue ==

HOOMD-blue is notable and comparable to LAMMPS.

hoomd-blue.readthedocs.io/en/stable/index.html#

It is mentioned here: [[Molecular modeling on GPUs]] and deserves a page of its own.