No module named 'MDAnalysis.analysis.msd'

[Ahmadreza Motezakker (Alumni)]

Dear All,

I am trying to use msd function of MDAnalysis and I face below error:

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No module named 'MDAnalysis.analysis.msd'

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after running below lines

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import MDAnalysis as mda

import MDAnalysis.analysis.msd as msd

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I have uninstalled MDAnalysis and installed again with no result. I really appreciate your help.

Best Regards

[irfan....@googlemail.com]

Hi,

What version of MDAnalysis do you have installed?

The MSD analysis code is only available in the current development version of MDAnalysis.

Best regards,

Irfan

[Suliman Sharif]

There seem to be two versions of the docs going around that causes confusion pretty frequently.

MDAnalysis dev2.0.0 and MDAnalysis1.0.0.

When you google things the dev2.0.0 actually shows up more frequently than the 1.0.0 doc so somethings have shifted or introduced.

For the dev2.0.0 code I did something like this and I also just made it a completely new environment that way I have both 1.0.0 code and 2.0.0 code in case something breaks and I need to revert back:

conda create -n mdpython2.0 python=3.6

Make sure you don't have any of the previous MDAnalysis stuff is uninstalled. Clone the repo:

git clone https://github.com/MDAnalysis/mdanalysis.git

Check that you are on the correct branch

cd mdanalysis

git branch 

>>> *develop

If that's all correct then try out 

cd mdanalysis/packages

mdpython -m pip install -e .

The -e flag opens it in the editable mode so that if modifications are made it's reflected in your environment in real time. The period at the end tells the pip package manager that the setup scripts for MDAnalysis are here and it will automatically

execute the setup.py file.

See if that works, that's what I did to get on their dev branch.

-Sul

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Suliman Sharif

M.Sc Medicinal Chemistry | University of California, Riverside

B.Sc. Biochemistry | University of Texas at Austin

sharifs...@gmail.com

[irfan....@googlemail.com]

>  There seem to be two versions of the docs going around that causes confusion pretty frequently.

This is pseudo-intentional. We build both the docs for MDAnalysis spanning from 0.20.1 to the current developer version. This way folks using any of the version of MDAnalysis can have access to the docs.

I don't _think_ that there is a way we can enforce any of the docs to show up specifically on a search. Google will index what it wants however it wants unfortunately.

@Lily can correct me here.

Please note that we also have detailed install instructions for the developer version of MDAnalysis here: https://userguide.mdanalysis.org/stable/contributing_code.html#building-mdanalysis

To use the MSD analysis code you will probably want to install the `tidynamics` optional dependency.

Best regards,

Irfan

[Ahmadreza Motezakker (Alumni)]

Dear Irfan/ Dear Suliman,

Thank you very much for your help. I did the steps Suliman mentioned and it worked. 

Best regards,

Ahmad Raez

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