[gmx-users] Updated tutorials and new website

[Oliver Beckstein]

Hi,

Justin's tutorials are really a great boon to the community (and to new students joining my group – they are part of our introductory “bootcamp”). It would be nice to also have a “community” repository of repositories, especially with some templates or structure that other could follow.

A while back we started a tutorial on simulating the globular enzyme AdK in solution https://adkgromacstutorial.readthedocs.io <https://adkgromacstutorial.readthedocs.io/> (but it’s not always been kept up-to-date (this is hard – kudos to Justin for doing it for his tutorials!). It was written in restructured text and built with sphinx and automatically published on ReadTheDocs, i.e., publishing the pages and hosting could be done automatically. If combined with basic continuous integration that checks that a PR builds the docs nicely then one might be able to turn this into a framework for community-based tutorials.

Anyone who wants to use this as a starting point: Please feel free to use anything in https://github.com/Becksteinlab/AdKGromacsTutorial <https://github.com/Becksteinlab/AdKGromacsTutorial> (we added a BSD-3 license but we change it to whatever is necessary).

Oliver


> On Jun 30, 2018, at 9:11 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> A great contribution would be to write some for your own area of expertise.
> Or with similar content but done in a different way.
> 
> Mark
> 
> On Sat, Jun 30, 2018, 02:42 paul buscemi <pbuscemi at q.com> wrote:
> 
>> Justin,
>> 
>> Thank you for all the hard work !   What can we do in return ???
>> 
>> Paul
>> 
>>> On Jun 29, 2018, at 5:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> 
>>> 
>>> Hi All,
>>> 
>>> I have updated all of my tutorials for use with GROMACS 2018. They are
>> now hosted on a new site:
>>> 
>>> http://www.mdtutorials.com/gmx/
>>> 
>>> The tutorials currently hosted on bevanlab.biochem.vt.edu will be
>> permanently taken offline by the end of the summer. I realize that many
>> other sites link to these tutorials, so please update links and bookmarks
>> if possible. In the meantime, the old tutorials will redirect to the new
>> ones.
>>> 
>>> I hope the new tutorials will be helpful - there are many new and
>> improved sections, and the protein-ligand tutorial has essentially been
>> completely rewritten with a newer approach and different force field. I
>> apologize if there are any difficulties due to links that will now break,
>> but the situation is unavoidable due to the permanent decommissioning of
>> the Bevan lab server.
>>> 
>>> Please let me know if there are any difficulties with the new tutorials
>> or website.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==================================================
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>> 
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>> 
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>> 
>>> ==================================================
>>> 
>>> --
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--
Oliver Beckstein, DPhil * oliver.beckstein at asu.edu
https://becksteinlab.physics.asu.edu/

Associate Professor of Physics
Arizona State University
Center for Biological Physics and Department of Physics
Tempe, AZ 85287-1504
USA
	
Office: PSF 348
Phone: +1 (480) 727-9765
FAX: +1 (480) 965-4669

Department of Physics: https://physics.asu.edu/content/oliver-beckstein
Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein