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marrink-lab / bentopy

Packs stuff in boxes
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Add relevant topol_includes to the README example #9

Open ma3ke opened 5 months ago

ma3ke commented 5 months ago

Currently, the README is rather vague and unhelpful regarding the topol_incudes in the input configuration.

It would be better if a relevant force field is used here. I have worked with that in the case of Martini structures, but not for AA force fields.

Also relates to #3 and #6, of course.

ma3ke commented 5 months ago

In fact, @jan-stevens and @BartBruininks, do you have an idea of expressing this well in a simple README usage example without going too in-depth? (Wouldn't want to explain here how to set up the 3lyz.itp file, for example.)

Perhaps this fits better with an actual tutorial (#3). There I'd be happy to go a bit deeper into that. But for the README, we want to only discuss bentopy and its features/usage without getting distracted. But leaving this detail out completely would be incorrect too.

The point is that topol_includes is necessary for most use-cases of bentopy, but does not really relate to what bentopy itself does.

BartBruininks commented 5 months ago

I think it's best to state pdb2gmx or charmmgui can be used to get the itp for AA proteins. Since we are focusing on GRO, I do not think it is strange that we assume that people heard about gromacs. For cg martini one can use martinize2 etc. Bottom line. In the readme, assume the .itp exists and continue with your life. In a tutorial you can show how to get the itp for the specific case you are demonstrating.

ma3ke commented 5 months ago

Sounds good, I agree. Thanks!