Rotating molecules in Powerpoint - part 2

Animation in Powerpoint
One of the most accessed posts on this blog is Rotating molecules in Powerpoint.  I wrote the post more than a year ago, and had I written the post today it would be different thanks to a great free program called Screencast-o-matic.

The screencast above shows how to use Screencast-o-matic to make short movies of rotating molecules and other molecular animation and include them in Powerpoint presentations.

Jmol in Powerpoint
A lot of people end up on this blog by searching for "Jmol in in Powerpoint" or some similar term.  As far as I know it is not possible to embed Jmol in Powerpoint slides.  It is possible in Beamer, as discussed in this post by Janus Eriksen.

Using Screencast-o-matic you of course record any sequence of Jmol animations, but it will not be interactive.  Personally, I make a web page with my Jmol model, with buttons to control what I want to do and simply switch between Powerpoint and a browser.  I give a short example using this Jmol model in the screencast below.

Blurring the boundary between linear scaling QM, QM/MM and polarizable force fields Part 2

My talk at WATOC 2011.  Slides can be found here

Here's how I made the video: I recorded my talk using the Voice Memo app on my iPhone.  Then I replayed the talk on my Mac using iTunes as I went through my slides on Powerpoint.  I recorded the screencast + audio using Screenflow.

Thanks to Anders Christensen for recording the video.

Summarizing a paper using Prezi and Screencast-o-matic

In a previous post I summarized a paper using two programs: Prezi and Screencast-o-matic.  Both are free and easy to use.  The screencast above shows how I did it. Anyone can do this.

I did this on a mac, so I used the earphones/microphone that came with my iPhone.  The sound is not the greatest, but good enough I think.

The screencast is 9 minutes long, which might be too long.  It's hard to strike a balance between detail and the big picture.  Hopefully, I will improve with time.  Feedback is very welcome.

Update: be sure to check out the comments below

New paper: Ring current effects in proteins

Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

Anders S. Christensen*, Stephan P. A. Sauer, and Jan H. Jensen*

Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark

J. Chem. Theory Comput., 2011, 7 (7), pp 2078–2084

DOI: 10.1021/ct2002607

Abstract (the paper is summarized in the video at the end of the post)
The ring current effect on chemical shifts of amide protons (Δδ_RC) is computed at the B3LYP/6-311++G(d,p)//B3LYP/aug-cc-pVTZ level of theory for 932 geometries of dimers of N-methylacetamide and aromatic amino acid side chains extracted from 21 different proteins. These Δδ_RC values are scaled by 1.074, based on MP2/cc-pVQZ//B3LYP/aug-cc-pVTZ chemical shift calculations on four representative formamide/benzene dimers, and are judged to be accurate to within 0.1 ppm based on CCSD(T)/CBS//B3LYP/aug-cc-pVTZ calculations on formamide. The 932 scaled Δδ_RC values are used to benchmark three empirical ring current models, including the Haigh–Mallion model used in the SPARTA, SHIFTX, and SHIFTS chemical shift prediction codes. Though the RMSDs for these three models are below 0.1 ppm, deviations up to 0.29 ppm are found, but these can be decreased to below 0.1 ppm by changing a single parameter. The simple point-dipole model is found to perform just as well as the more complicated Haigh–Mallion and Johnson–Bovey models.

The paper Instructions on how I made the video will appear in a future post. In the mean time, enjoy!

Blurring the boundary between linear scaling QM, QM/MM and polarizable force fields

Jan Jensen's presentation at WATOC 2011

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Thursday morning, room B

Update: a recording of the talk can be found here

Peer instruction: mixing

Peer instruction questions: mixing

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These slides show questions I used when teaching mixing functions using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

Some comments about specific slides:
Slides 1-3 show results from a Molecular Workbench simulation, which you access here.  It is a variation on the simulation I used to illustrate entropy.  If you understand why the gas expands in that example, you also understand why the gasses mix.

Slides 4-10 show results from a Molecular Workbench simulation, which you access here.

Slides 4-5: after two votes there was no clear consensus, but most students likes A "no interactions between molecules".  The second vote came at the end of the first of three back-to-back lectures, so we had a third vote after the break.  There really was intense discussion of this during the break, when most finally settled on B "equal interactions between molecules".   I think A was popular because "ideal solution" conjures up an analogy to "ideal gas", but how can you have a liquid if there are no intermolecular attractions?

Slide 7-8: here is alternated between the simulation and the question a few times.  A better approach would have been to include the question on the web site with the simulation.

Related blog posts
See all posts related to peer instruction here.
Illustrating mixing
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Peer instruction: radial distribution functions

Peer instruction questions for radial distribution functions

View more presentations from molmodbasics

These slides show questions I used when teaching radial distribution functions using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

Some comments about specific slides:
Slide 8: The hint is given after the first vote.

Slides 11-18 show results from two Molecular Workbench exercises, which you can download here and here, once you have installed Molecular Workbench on your computer.

Slide 11: First I run the solid simulation, then pose the question and have a couple of votes, then click on the "show pair correlation function" in the MW simulation.  Note that you have to run for at least 100,000 fs to get good statistics (i.e. relatively smooth curves).  Then I explain the answer (slides 12 and 13)

Slide 14: Same procedure as slide 11, but for the liquid.

Slide 16: No vote, since the answer is pretty obvious, but I do ask where the peak at r = ~1.5 Å comes from.  Of course it comes from the attractive part of the Lennard-Jones potential, and you can clearly see some particles sticking together in the gas simulation.  To check, I change the depth of the well from 0.1 eV to 0.001 eV (simply double-click on any of the particles, and you will see what to do), re-run the simulation, and show the radial distribution function (summarized in slide 17).

See all posts related to peer instruction here.