Mining VSITEN bonds from TPR files

[d-beltran]

Hi everyone,

I am having problems while reading a TPR file since VSITEN bonds are ignored.
Maybe I am doing it wrong or I have to enable some setting?

If this is not possible, is there any chance that PR #4318 could fix this?

And if not, do you think the discussion in #1954 will be resumed any time soon?

Thank you and best regards

[orbeckst]

There hasn't been any progress on reading VSITES from TPR so I don't think a solution will materialize any time soon. You can certainly try out #4318 and contribute to the discussion in #1954 .

The only thing I can say in a situation like this: MDAnalysis open source, it is "written by scientists for scientists", and thus is driven by its users in the sense that users become contributors when they are solving a problem that's important to them. Start digging into the TPR code, PR #4318 and see if you can come up with a solution. Start looking into how MDA represents particles and contribute to the discussion.

For a start, you could add your voice to #1954 and explain how you as user would expect vsites to be handled in MDA. What would you want to do?

The lack of activity typically indicates that the issue is not a burning problem for the core development team and there isn't a huge demand in the community. Experience shows that most features really need one person as a champion to keep working on them and then they will eventually make it into the code. It's just a process with many facets.

Discord or the discussions here is a good starting point to ask questions on how to get started. Most of the technical discussions happen on pull requests as discussions about concrete code are more focused and productive.