[gmx-users] Updated tutorials and new website

Tue Jul 3 13:44:17 CEST 2018

Hi Justin,

that sounds like a great plan.  Thanks for initiating something like this.

Iris,

I am up for helping with some of the tutorials, especially, the ED
simulations if you need any help. That is something I have some experience
with as well.

Shreyas

On Tue, Jul 3, 2018 at 1:13 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
> 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
> >>>>>>
> >>>>>> ==================================================
> >>>>>>
> >>>>>> --
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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 <+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
> >> --
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> --
> ==================================================
>
> 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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-- 
Shreyas Sanjay Kaptan