Concepts to cover

FAQ

These notes are gathered from every post in mdnalysis-discussion from October 1st 2018 to August 21st 2019 (UTC).

Out of 133 posts, these were the broad topics:

• Analysis (42)
• Universe I/O (18)
• Irrelevant, i.e. not about MDAnalysis (14)
• Google Summer of Code (11)
• Topology (9)
• AtomGroup (9)
• Selection (9)
• Package stuff (5)
• Installation (4)
• Trajectory (3)
• PMDA/large data (2)
• Questions due to updates (2)
• Development (2)
• Getting started (1)
• Units (1)
• Universe dimensions (1)

Analysis

Understandably, questions about analysis were the largest proportion. These loosely fell into several subcategories:

• Analysis (running) (13)
• Custom analysis (general) (11)
• Analysis (method) (7)
• Analysis (general) (5)
• Custom analysis (method) (7)
• Analysis (output) (2)

Analysis (running)

These questions revolved details of how to actually use analyses that exist, e.g. RMSD without alignment step. It includes questions where certain topology attributes are required for the analysis that are not always in every file format.

Custom analysis (general)

Most of these questions were asking whether certain analysis methods existed, or how to implement them. This indicates a need for an easy index of available analyses and a tutorial of how to create your own functions.

Analysis (method)

These questions were based off not understanding what is happening under the hood of an analysis, e.g. radial distribution function, average over trajectory?

Analysis (general)

These questions asked how to do analysis that does exist, pointing to difficulty wading through the documentation and/or the need for easily digestible notebooks.

Custom analysis (method)

These were methodology questions in implementing custom functions.

Analysis (output)

Confusion about what output the analysis actually produces.

Universe