[gmx-users] [EXT] Re: Updated tutorials and new website
Smith, Iris
smithi4 at ccf.org
Mon Jul 2 22:59:31 CEST 2018
Dear Shreyas,
If you'd like to contact me offline (smithi4 at ccf.org) we can work on and compile useful tutorials together.
I can help with topics (3) and (4). I've analyzed protein-apo systems utilizing essential dynamics, so I'm happy to contribute in writing a tutorial. I'm currently working on building membrane system and will ultimately be doing QM/MM to refine some ligand parameters for a protein-membrane-ligand complex. I have had success with QM/MM ligand refinement in a protein-ligand only system - so I can help with writing up a useful tutorial. I can reach out to my friend who has been successful in setting up and running REMD systems [topic (2)] - he may have his protocol previously saved.
Iris
Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute
Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH 44195 | (216) 445-7885
On 7/2/18, 4:42 PM, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Shreyas Kaptan" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of shreyaskaptan at gmail.com> wrote:
Dear Iris,
that sounds like a great idea. I would like to ask what topics would be
considered useful for tutorials. I can think of a few:
1. Fast thermodynamic integration for alchemical transformations with the
CGI method with hybrid topologies for more complex examples
2. Replica exchange methods
3. An Essential dynamics tutorial
4. QM/MM tutorial (is that still viable ?)
5. Computational electrophysiology setup example from scratch?
I must admit I am myself very interested in some of these (especially the
QM/MM setups) and would like to see them in an accessible manner. For other
techniques, like CompEL, Essential dynamics, I am concerned that they are
underused by the community because no concrete tutorials for them exist.
If necessary I would help in setting some of these up if there is enough
demand.
Shreyas
On Mon, Jul 2, 2018 at 8:34 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/2/18 2:13 PM, Smith, Iris wrote:
> > That's a great idea Mark!
> > Should we submit these to you or Justin?
>
> Everyone has always been welcome to write and publish whatever tutorials
> they might come up with, and link them to the Tutorials page of
> gromacs.org. My new website is part of a publishing effort (coming soon,
> later this summer) and I'm not presently prepared to review submissions
> for inclusion. It's something I may think about in the future if there
> is sufficient interest, but probably not right now.
>
> -Justin
>
> > Iris
> >
> > Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute
> > Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH 44195
> | (216) 445-7885
> >
> >
> >
> > On 6/30/18, 12:11 PM, "
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Mark
> Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> 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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> --
> ==================================================
>
> 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
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