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Concepts to cover

Lily Wang edited this page Aug 31, 2019 · 8 revisions

FAQ

These notes are gathered from every post in mdnalysis-discussion from October 1st 2018 to August 21st 2019 (UTC). Release 0.19.0 came out on October 10th, 2018.

Out of 133 posts, these were the broad topics:

Analysis

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

Category # Notes Solution Links              
Analysis (running) 13 These questions revolved details of how to actually use analyses that exist. It includes questions where certain topology attributes are required for the analysis that are not always in every file format. Indexed list of modular notebooks
Custom analysis (general) 11 Most of these questions were asking whether certain analysis methods existed, or how to implement them. Above indexed list, also tutorial for custom analyses
Analysis (method) 7 These questions were based off not understanding what is happening under the hood of an analysis User guide pages with description of method as well as how to use it
Analysis (general) 5 These questions asked how to do analysis that does exist. Digestible, understandable notebooks
Custom analysis (method) 7 These were methodology questions in implementing custom functions. User page explaining base analysis class. Some questions were more about understanding Python/MD, which can't be helped.
Analysis (output) 2 Confusion about what output the analysis actually produces. Notebooks

Universe

Category # Notes Solution Links
Format (general) 4 How to use formats that MDAnalysis has defined. Notebooks
Format behaviour 3 How MDA treats formats Notes on MD format pages about their behaviour
Other formats 3 I/O with custom formats, e.g. Numpy or GridData Cover this in I/O page
Incompatible format 2 How formats work Notes on MD format pages about their behaviour
Write trajectory 2 How to write a trajectory Notebook and in Quickstart guide
Memory 2 Problems with large data Notes on how memory works in MDAnalysis, and pointer to PMDA
Paths 2 Python/path issue Add a note in a notebook "Change this for your file"
General MD 1 Mismatch between TPR and GRO Perhaps mention this as a possibility?
Trajectory slicing 1 Loading in a trajectory in steps Note that this isn't possible.

Topology

Category # Notes Solution Links
Adding TopologyAttr 4 How to add topology attributes -- especially bfactor vs tempfactor. Describe this in a Topology Manipulation section, as well as having examples in notebooks as a way to visualise analysis.
Guessing topology information 3 Guessing bonds or elements. Be clear about what is/can be guessed.
Modifying bonds 2 How to add, remove, or modify bonds. Topology manipulation section
Adding segment 1 How to add new segments. Document this with other Group editing.

Selection

Category # Notes Solution Links
Selection command 4 Which string to use to get desired atom groups. A comprehensive page on atom selection language -- this is as much MD knowledge as MDAnalysis.
Proper selection group 2 How to select the right AtomGroup for the analysis. Notes on selection on the specific analysis pages.
Using GROMACS index 1 Can we use .ndx files to select? No, but awesome idea.
Dynamic evaluation 1 Does the selection update over the analysis? Yes, needs a note on the analysis page.
Ranked selection 1 Selecting the 10 nearest atoms. The solution is neat and could be a notebook.

AtomGroup / ResidueGroup

Category # Notes Solution Links
Transformation 2 How to transform molecules. A notebook on transformations
Attributes 2 Getting/setting attributes A concise API reference
Group behaviour 1 OOP behaviour Describe clearly how Groups work in docs.

Universe

Category # Notes Solution Links
System building 2 Building molecules from coordinates by assigning TopologyAttrs Include this in system building documentation
Universe dimensions 1 Universe attributes Concise API reference

Other

Category # Notes Solution Links
Trajectory 2 Dealing with dynamic positions Point out positions changes and detail consequences.
PMDA 2 Dealing with large data Outside the scope of this guide. Link to PMDA docs.
Unit transformation 1 Transforming LJ units to conventional units Possibly include this in the Units page.
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