User talk:Dacb

Dynameomics

Hi,

The weblink you are persistently trying to add to the page Molecular dynamics does not belong there. The article deals with molecular dynamics techniques in general and the list of software for MD simulations is a collection of major projects that could/should be of use to others, i.e. that are of some notoriety and freely available.

The external links are websites about molecular dynamics in general and not just a collection of projects that have or use molecular dynamics. According to the site you linked,

“ Dynameomics is a continuing project in the Daggett group to characterize the native state dynamics and the folding / unfolding pathway of representatives from all known protein folds by molecular dynamics simulation. ”

That does not qualify as molecular dynamics in general and would be better suited in the links on Molecular modelling, Protein folding or Protein structure prediction.

Cheers and kind regards, pedro gonnet - talk - 31.10.2007 08:22

Pedro,

Regarding the software section: It would be appropriate for the heading to be retitled to something that fits that section's apparent criteria. That is, by what criteria are those 'Major software'? By publication count? By number of labs using the software? It might be better to have an expert in the field decide what is or isn't considered 'major'. Furthermore, 'the freely available' constraint is a red herring as not all of those packages ARE freely available (i.e. they require payment in order to obtain a license as does ilmm) and why should a section entitled 'Major software' be limited to only those packages that are released under the GPL?

Regarding the links section: I see you have removed all of the web sites that store and share MD trajectories which is a shame. Again, the criteria for that section seem arbitrary. Certainly you wouldn't remove the BMRB link from the Nuclear Magnetic Resonance page simply because the site wharehouses data rather than explains the technique.

I suggest modifying the section titles to reflect your 'personal' criteria or simply allow the page to grow under expert supervision.

- dacb

Hi dacb,

I'll answer point for point to keep things a bit structured:

• Major Software: There is, of course, no official definition. What the software packages currently in the list have in common, is that they are used by people other than those who developed it. A quick look on Google and ISIKnowledge show that this is not really the case -- all publications using ilmm are co-authored by Prof. Daggett. In any case, if the software is indeed used outside the Daggett-group (excluding people explicitly collaborating with the Daggett group), then you should add a link to the simulation software itself.
• Freely available: There is no link to donwload the software or notes on how to obtain it, neither on the Dynameomics site you linked or the ilmm site. Beyond being freely available, there is nothing to indicate that this software is available at all.
• Sites sharing trajectories: Seriously, would you expect a link to a list of bridges designed using Finite elements in that article? There are more specific artcles (the ones I mentioned above) where such sites would be much more at home. You may even consider starting an article on Molecular dynamics trajectories which could be linked in the subsection "See also".
• NMR-Trajectories: First of all, I am not responsible for the Nuclear Magnetic Resonance article. Secondly, that is one site in a list of about 20 and it contains more than just the trajectories.
• Personal criteria: Judging by your edit history and your comments, you seem to be new to Wikipedia. You may want to take a look at WP:NOT, WP:NOTE and WP:COI (if you are not new, you might want to re-read WP:SPA ;) ). I don't know if I could consider myself an "expert" in the field (that is a title usually attributed by others, not by oneself), I do, however, have a degree in Computer Science and a minor in Biochemistry and several years experience doing simulations and research in simulation algorithms in an academic environment and even have some publications to that extent. You are not talking to a complete newbie.

If you think you can get consensus on the inclusion of your links, then we should take this discussion to Talk:Molecular dynamics. I only took this issue up with you personally because I thought there might have been some misunderstanding on behalf of a newcommer (see WP:BITE and WP:AGF).

Cheers, pedro gonnet - talk - 01.11.2007 10:06