To do items for a subsequent revision (?)

MobleyLab / basic_simulation_training

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be required for understanding/following many of the other "best practices" documents being prepared.

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To do items for a subsequent revision (?) #71

Open davidlmobley opened 6 years ago

davidlmobley commented 6 years ago

Things it doesn't seem like we will get to for our initial version, but which would probably be good to include:

"Blowing up" as a symptom of deeper problems/energy minimization issues; I can't tell you how many times I've had students spend a lot of time trying to figure out what's wrong with their constraint algorithm, when really that's just a symptom of the underlying problem (inadequate minimization, or a setup which is fundamentally flawed -- molecules sitting on top of each other, bad bonds, etc.).
Make sure we reference appropriate Leimkuhler work on integrators

JIMonroe commented 6 years ago

Add more references to integrators section, especially good comparisons of properties such as accuracy (phase-space preservation), and energy conservation. Unbiased reviews not associated with methods development would be ideal, but as these seem rare a carefully-selected set of papers from the field would be appropriate.

davidlmobley commented 6 years ago

Provide a list of all the abbreviations/symbols.