[gmx-users] Updated tutorials and new website

Tue Jul 3 13:13:22 CEST 2018

The enthusiasm for writing new tutorials is very encouraging, and 
admittedly has taken me a bit by surprise. Let me "pull back the 
curtain" on what I am thinking regarding my own site and how others 
might engage.

I am about to submit an article detailing my tutorials and the 
theoretical underpinnings of them and context within the existing 
literature. Writing this article spurred me to make the move to a new 
server (which was inevitable, anyway) and update everything for version 
2018. The paper is being submitted to LiveCoMS 
(http://www.livecomsjournal.org/), which is built upon "living" articles 
that can be revised and updated over time, with each new major version 
being a new submission and new article. If people haven't heard about 
it, please check them out. The source file and content of my article 
will be available on GitHub soon.

For those interested in hosting something on my site, I'm open to 
proposals. I won't be adding anything new until after my article is out 
(it is far too late for anyone to try to contribute anything to it, 
anyway, as the article will be submitted within a few days) but for 
anything after that, please let me know what you might write. I wrote 
all of my tutorials based on things I was actively doing in my 
dissertation work, so it was natural for me to share with everyone what 
I had learned. I encourage others to do the same.

The tutorial site is also a large part of a very important grant I will 
be submitting that needs to include educational components, so please 
understand and expect that I will have certain standards for inclusion, 
because as I have learned over the last 10 years of effort, it is no 
small task to write and maintain high-quality tutorial material. I 
haven't exactly formulated how all of that will work out, but anyone 
with a solid idea and the drive to write a tutorial is welcome to reach 
out to me. While I have contributed some code to GROMACS over the years, 
my biggest contribution is obviously in documentation and teaching, 
which I enjoy doing and will continue to do in support of this community 
and the important science that people are doing.

If people want to continue the discussion here, that's great and I'll 
comment as needed, or feel free to send ideas to me off-list.

-Justin

On 7/3/18 4:28 AM, Mark Abraham wrote:
> Hi,
>
> We have several new tutorials from the core/BioExcel team also (done as
> Jupyter notebooks) that we plan to make available, though I have not
> thought much yet about the form of delivery.
>
> Obviously the GROMACS website is overdue for renovation (and yes, that's on
> my to-do list), but we're very happy to make a central home for content
> people would prefer to host there.
>
> As Oliver notes, some basic CI testing is really nice for smoothing over
> version differences, so I particularly encourage authors to record some
> kind of script (bash, python, whatever suits you) that enables the
> regeneration of any saved output from GROMACS, or other tools. Then when we
> publish new versions of GROMACS it's straightforward to update the content
> as needed, and that can evolve into a useful framework. There's also ways
> to embed lightweight molecular viewers in web pages and Jupyter notebooks,
> which helps avoid classes of students needing to deal also with vmd or
> pymol in their first rodeo...
>
> Mark
>
> On Tue, Jul 3, 2018 at 7:01 AM David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
>> Den 2018-07-03 kl. 03:32, skrev 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).
>>
>> Maybe it would be good to merge these kind of efforts into one
>> gromacstutorial.readthedocs.io
>> and
>> gromacstutorial.github.com
>>
>> Volunteers?
>>
>>> 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
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>>
>>> --
>>> 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 <+1%20480-727-9765>
>>> FAX: +1 (480) 965-4669 <+1%20480-965-4669>
>>>
>>> Department of Physics: https://physics.asu.edu/content/oliver-beckstein
>>> Center for Biological Physics:
>> https://cbp.asu.edu/content/oliver-beckstein
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005>
>> .
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.

-- 
==================================================

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

==================================================