Create separate tutorial for "advanced" AdK Gromacs Tutorial?

[sseyler]

Overview

The initial version of the tutorial that is live on RTD as of March 28, 2017 is a basic version that could be followed by anyone, in principle. The purpose of the advanced tutorial would be to make it as simple as possible for lab members to get familiar with Gromacs, with the useful side-effect of generating data that could be used for publication. To create the advanced AdK Gromacs tutorial, I intend to piece together the scripts I've used (also Taylor) for AdK simulations. This advanced version should:

• Do proper multi-step minimization/equilibration
• Include the bash scripts that help automate the process—from system setup to production runs—to ensure consistency of results
• Have details and information that would be specific to (new) members of Becksteinlab (e.g., module load gromacs/5.1.3/...)
• Other things I might have forgotten

Separate repository?

I'm not sure if we should have a separate repository for this version. On the one hand, it may be easier to maintain separate repos, make it easier to deal with Read the Docs by keeping each tutorial cleaner (fewer toctree levels), and allow the current basic tutorial to stand on its own so that others outside the lab can use it. On the other hand, it seems a bit excessive to have, say, "AdKGromacsTutorialBasic" and "AdKGromacsTutorialAdvanced"; also, Gromacs tutorials already exist, so we'd only really be offering an alternative. Any thoughts on the matter?

[orbeckst]

I would keep it all together. Then a student can stay within the AdK tutorial to progress from beginner to intermediate and advanced.

[sseyler]

Okay, I'll think about how I want to organize things to keep the docs clean.