What other materials are needed?

[davidlmobley]

@kofke - from your course website, it looks like you have a pretty good base amount of material already ready but I notice there are some things you do not yet have that are for your course in particular:

• Measuring dynamical properties
• Isothermal/isobaric MD
• Dielectrics
• Simulating molecules
• Free energy calculations

Should I see what I can do in terms of finding and/or generating content for those? For example, Scott Shell's course has material which provides at least some of this content and he's agreed to let us adapt/use/extend here, so that could provide a starting point to put in here and edit from, if you're amenable.

But presumably there are other topics we would want to cover eventually that your course does not touch on but which are nevertheless relevant. For example, my course (which I have to keep in mind) also covers or at least touches on:

• QM background of force fields and where force fields come from
• Fluctuations, correlations, and error analysis (Zuckerman may also have good materials we can draw on for this)
• Biomolecular simulations: How to assess experimental data inputs such as crystal structures
• Visualization of simulations and movie-making
• Energy minimization algorithms

There are also aspects of the course not as much relevant to molecular simulations that focus on library searching, docking, screening, etc. for small molecules.

[kofke]

The way that I wrote the material is to take the Powerpoint lessons and to add text that more-or-less narrates them. This takes advantage of the organization already in place in the lesson, and the figures can be dropped in from the ppt file. Presumably I could do that for the other topics, when time permits. Still, it would be great if you found material for those, so if something comes up, do go ahead.

The second set of topics would make sense too, of course, and aren't something I'd be likely to do, so they'd be a good place for you to focus your efforts.

I do have material on uncertainty and error analysis, and that was the next thing I was working on before getting caught up in other things. I'm giving a workshop on the topic at the end of the month, so I'm motivated to give it more attention. The material being put together by the Error Analysis group is focused on best practices, and maybe less on fundamental concepts, so this could be complementary to that.

[davidlmobley]

@kofke - sounds great, thanks. I do think this is very complementary to the things being done by the Best Practices groups -- my hope is that things we put together here would be material they might want to link out to as freely available useful background reading.

Tagging @dmzuckerman in case he has materials he might want to contribute or things he would suggest we draw on.

[dmzuckerman]

@kofke @davidlmobley - this could really be a valuable project once everything gets put in place.

I don't think I have anything that I can contribute immediately. For teaching stat mech, I am a big fan of using very simple (one-dimensional when possible) and generalizing from there, which is the strategy I use in my textbook.

David K is correct about this: "The material being put together by the Error Analysis group is focused on best practices, and maybe less on fundamental concepts."

I was just thinking today that it would be useful to have a simple resource on non-eq stat mech. I have been leading a study group on this, starting from the diffusion equation. I might like to try to write that up one day, but not sure when.

I do have a (perpetually) in-progress online textbook on biophysics useful for cell biology, which might give you guys some ideas for staging.