BioSimSpaceTutorials

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Questions and todo's as they arise around the FEP tutorial

13

I am using this issue to help with merging [this](https://github.com/michellab/BioSimSpaceTutorials/tree/main/04_fep) and [this](https://github.com/michellab/bssccpbiosim2022) set of FEP tutorials. I'll keep updating to dos adding questions etc. Questions: - [x] We keep the...

ppxasjsm

making all tutorials uniform using a common style guide

6

@lohedges, @annamherz @jmichel80 @fjclark @AdeleHardie @dlukauskis, I have created a style guide here: https://github.com/michellab/BioSimSpaceTutorials/blob/main/Style_guide.ipynb Can you look over it and let me know what you think. It would be good...

ppxasjsm

This repository is massive

5

Are all of the files in this repository strictly necessary for the purposes of the tutorials. I've just done a fresh clone and see the following... The compressed repository size:...

lohedges

Posting already but will edit more to fill in details in abit. Text: General readme: - [ ] Make sure it contains all essential information including installation etc. It seems...

ppxasjsm

ABFE

1

I have performed funnel metadynamics simulation using the Biosimspace. During ABFE calculation, I am a little bit confused. As in the tutorial file "https://github.com/michellab/BioSimSpaceTutorials/blob/main/02_funnel_metad/03_bss-fun-metad-analysis.ipynb" mentioning the: # the last 0.5...

rubinanoor9

FEP tutorial comments

18

Hi @JenkeScheen , A few comments/questions after going through your setup notebook: - The notebook assumes the user has access to parameterised ligands (in vacuum) that have coordinates matching those...

jmichel80