Talk:Comparison of software for molecular mechanics modeling

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. --h (talk) 16:51, 5 July 2023 (UTC)

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? —Preceding unsigned comment added by 129.186.148.15 (talk) 14:00, 17 September 2010 (UTC)

2) "DL_POLY" software, which is quite popular, is missing. — Preceding unsigned comment added by 93.180.12.98 (talk) 10:50, 19 June 2012 (UTC)

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?

JKW (talk) 22:20, 11 November 2008 (UTC)

:Well each entry is linked to its own article, which presumably has references, or it it is linked to a reference. What else do you want? --Bduke (Discussion) 01:55, 12 November 2008 (UTC)

::I think it is a good idea to always provide references (the original reference in, say, PubMed). This is because not every website makes it easy to find the associated references. I would suggest using an abbreviated form. Something like: [http://dx.doi.org/10.1016%2FS0263-7855%2898%2980030-1 Bacon D, et al., 1998] (for Raster3D and where the link is the DOI number). I also suggest we try to add all of the license types to each entry. --Thorwald (talk) 04:28, 12 November 2008 (UTC)

The following list was taken from the Molecular dynamics#Major software for MD simulations section of that article. Some of these do not appear in this article and should be included:--Thorwald (talk) 21:35, 3 April 2009 (UTC)

• ABINIT (DFT)
• [http://cbbl.imim.es/Adun ADUN] (classical, P2P database for simulations)
• AMBER (classical)
• [http://www.agilemolecule.com/Products.html Ascalaph] (classical, GPU accelerated)
• CASTEP (DFT)
• CPMD (DFT)
• [http://cp2k.berlios.de/ CP2K] (DFT)
• CHARMM (classical, the pioneer in MD simulation, extensive analysis tools)
• [http://www.cosmos-software.de/ce_intro.html COSMOS] (classical and hybrid QM/MM, quantum-mechanical atomic charges with BPT)
• [http://www.DEShawResearch.com/resources.html Desmond] (classical, parallelization with up to thousands of CPU's)
• [http://www.ccp5.ac.uk/DL_POLY/ DL_POLY] (classical)
• ESPResSo (classical, coarse-grained, parallel, extensible)
• [http://fireball-dft.org Fireball] (tight-binding DFT)
• GROMACS (classical)
• GROMOS (classical)
• GULP (classical)
• [http://www.biowerkzeug.com/ Hippo] (classical)
• LAMMPS (classical, large-scale with spatial-decomposition of simulation domain for parallelism)
• MDynaMix (classical, parallel)
• [http://www.ccp5.ac.uk/moldy/moldy.html MOLDY] (classical, parallel) [http://ccpforge.cse.rl.ac.uk/frs/?group_id=34 latest release]
• [http://accelrys.com/products/materials-studio/ Materials Studio] (Forcite MD using COMPASS, Dreiding, Universal, cvff and pcff forcefields in serial or parallel, QMERA (QM+MD), ONESTEP (DFT), etc.)
• MOSCITO (classical)
• NAMD (classical, parallelization with up to thousands of CPU's)
• [http://www.univie.ac.at/newtonx/ NEWTON-X] (ab initio, surface-hopping dynamics)
• [http://protomol.sourceforge.net/ ProtoMol] (classical, extensible, includes multigrid electrostatics)
• PWscf (DFT)
• [http://www.sphinxlib.de S/PHI/nX] (DFT)
• SIESTA (DFT)
• VASP (DFT)
• TINKER (classical)
• [http://www.yasara.org YASARA] (classical)
• [http://www.chim.unifi.it/orac/ ORAC] (classical)
• XMD (classical)

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? --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. --Thorwald (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. --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). --Thorwald (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 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. --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. (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. (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. --Thorwald (talk) 21:02, 3 April 2009 (UTC)

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

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

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. Kadhgar (talk) 21:31, 29 July 2011 (UTC)

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. 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. P99am (talk) 13:17, 26 January 2012 (UTC)

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

Divof (talk) 16:59, 18 April 2014 (UTC)

this list should be coloredspecially the license column — Preceding unsigned comment added by 130.192.116.220 (talk) 16:07, 8 July 2014 (UTC)

Hi all,

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

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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. The Banner talk 07:32, 19 September 2019 (UTC)

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.