How to slice an existing universe at specified timeframe to create new universe?

[rayanc72]

Hi all, I would like to create smaller universes of different timeframes (e.g., 2 ps to 5 ps, 3 ps to 6 ps, and so on from an existing universe of 0 ps to 20 ps). What is the best way to achieve this only using the existing universe and without reading or writing any files?

[IAlibay]

@rayanc72 Do you mean that you want slices of your trajectory?

Would it work for you to just iterate your analysis over the specific sub sections of the trajectory as needed?

[rayanc72]

Thanks! Yes, that would work too. However, I could not find the syntax for that in the documentation. Specifically, I'm trying to use rdf.InterRDF_s at different timeframes. Do you have any suggestions on how to feed in specific sub-sections of the trajectory to this class?

[IAlibay]

@rayanc72 I believe that this class uses our standard AnalysisBase class type. To run your analysis over specific frames you can pass the start, stop, step arguments to the run method: https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#example-of-using-a-standard-analysis-tool

There's also a frames argument you can use to pass through a list of frame indices you want to use it that's more useful (it's detailed a bit lower in the above link).

[rayanc72]

Thank you! That works! 😅