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schrodinger / coordgenlibs

Schrodinger-developed 2D Coordinate Generation
BSD 3-Clause "New" or "Revised" License
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Write energy and coordinates to file to track force field minimization #94

Closed rachelnwalker closed 3 years ago

rachelnwalker commented 3 years ago

I made these changes to track the coordinates and energy of each atom in a molecule in each step of force field minimization. I found it useful in analyzing/viewing the minimization process. I'm not sure if we would actually want to merge this, but I wanted to make this PR just in case someone else would find this useful. If we do want to keep this, let me know what sort of #ifdef I should use.

Here is an animation of the minimization process I made with this data:

https://user-images.githubusercontent.com/39069546/116461830-95762d00-a81d-11eb-97b7-9907d7828bba.mov

ZontaNicola commented 3 years ago

this is super interesting, thank you! this also looks like the dof step is not doing its job, most of these clashes could have been prevented by flipping some of these side chains on the other side. Also I can see the energy does seem to go uphill and end up in a conformation that has a higher energy than some pretty early ones... I kind of like the final one better though

rachelnwalker commented 3 years ago

minimization_data.txt now includes coordinates from the avoidClashes step of coordinate generation. Here is an example animation where force field minimization is not required:

https://user-images.githubusercontent.com/39069546/117040571-e0c98900-acbe-11eb-9016-64d9d9e6b541.mp4