Concepts to cover

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 (42)
• Universe I/O (19)
• Irrelevant, i.e. not about MDAnalysis (14) (Not covered here)
• Google Summer of Code (11) (Not covered here)
• Topology (9)
• AtomGroup (9)
• Selection (9)
• Package stuff (5)
• Installation (4)
• Trajectory (2)
• 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.

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	Regarding MSD RMSD without alignment step Calculating electron density profiles of a lipid bilayer using linear density Encore clustering & RMSD matrix Replicate minimized RMSD using alignment Error with PMDA Very high values of RMSF analysis Help with hydrogen bond analysis Unable to get the donors and hydrogen's in Hydrogen bond auto-correlation function defining contacts (not based on cutoff) Resolving the matching of Donor and Hydrogen goup in Hydrogen bond auto-correlation function Hydrogen Bond Lifetimes issue? LinearDensity with an updating selection
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	Calculation of tetrahedral order parameter nan Cylindrical Average, cylindrical RDF How to calculate the volume of part of a pocket? Density profile in cylinder coordinate [mdanalysis-discussion] Contact Angle Angle of Rotation Fwd: MDAnalysis detecting surface residues script distance atom -slab problem the PBC box
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	Issue with atom selection radial distribution function, average over trajectory? Calculating distance moved per frame for specific molecules and saving the dataframe calculate volume of given group of atoms Helix Analysis interpretation MeanSquareDisplacement calculate diffusion of a single particle. RMSD difference between VMD and MDAnalysis
Analysis (general)	5	These questions asked how to do analysis that does exist.	Digestible, understandable notebooks	choosing the correct routines/analysis modules for diffusion coefficient. Regarding number of hydrogen bond Transform residues in PC1, PC2, and so on... problem center of mass and distance for center of carbon nanotube How to calculate minimum distance between two residues over a trajectory?
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.	(Bond) Vectors with pbc Possibility of getting an h-bond density Ramachandran plot with dynamic selection group (updating) Calculation of RDF from a NAMD DCD file
Analysis (output)	2	Confusion about what output the analysis actually produces.	Notebooks	Questions on the output (local_bend.xvg) of HELANAL calculations How to calculate the centre of mass of atoms between two different residue groups

Universe

Category	#	Notes	Solution	Links
Format (general)	4	How to use formats that MDAnalysis has defined.	Notebooks	Conversion of a gromacs trajectory into charmm trajectory Read LAMMPS XYZ and Velocity dump files Issue with time_offset attribute of Timestep class Read tor file to define universe
Format behaviour	3	How MDA treats formats	Notes on MD format pages about their behaviour	How chains/segments are distinguished Persistence Length of Polymer error count the number of a particular molecule in a xtd or xyz file
Other formats	3	I/O with custom formats, e.g. Numpy or GridData	Cover this in I/O page	analyse coarsened polymer Retain only ATOM entries when writing pdb file Density in Gaussian cube file format
Incompatible format	2	How formats work	Notes on MD format pages about their behaviour	Lamps dump with more than 5 atom_style arguments Loading .gro filetype trajectory
Write trajectory	2	How to write a trajectory	Notebook and in Quickstart guide	Regarding dat file fomating How to save coordinates array as a trajectory?
Memory	2	Problems with large data	Notes on how memory works in MDAnalysis, and pointer to PMDA	Issue with opening a NC trajectory file Loading very large trajectories
General MD	1	Mismatch between TPR and GRO	Perhaps mention this as a possibility?	Residue numbering changes from pdb to mda.universe
Paths	1	Python/path issue	Add a note in a notebook "Change this for your file"	Loading the gro and xtc file issues
Trajectory slicing	1	Loading in a trajectory in steps	Note that this isn't possible.	Slice universe when initializing it

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.	Assign additional attribute "name" to atom group Create a PDB file with the b-factor colored by RMSF -problem Adding new attributes to atoms Hydrogen bond calculation using lammps file format
Guessing topology information	2	Guessing bonds or elements.	Be clear about what is/can be guessed.	Generate topology attributes as bonds and angles Re: [mdnalysis-discussion] Assign additional attributes to atoms object
Modifying bonds	2	How to add, remove, or modify bonds.	Topology manipulation section	Remove/add bond and move atoms Changing bonds
Adding segment	1	How to add new segments.	Document this with other Group editing.	Add chain IDs to protein files