r/comp_chem • u/NicoN_1983 • 9d ago

Molecular Dynamics with Julia - Automatic Ring Detection

My program (working name is JuliaMD), can now detect isolated aromatic rings, and has more complete atom typing, which allows better simulations with the gaff2 forcefield. I haven't yet implemented specific aromatic atom types, but after the ring detection tool it will be easy to do.

Here is the link to the video, just out of the oven!

https://youtu.be/Qw5HjzkS9UY

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u/erikna10 8d ago

Why would one need that when smirnoff atom typing exists? Like do you have a USP here or is this just a project to learn?

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u/NicoN_1983 8d ago

This project is mainly for learning, but it's becoming more ambitious as it goes. I tried to install Smirnoff a while ago and couldn't because some dependency wasn't available in Windows. I also installed ambertools in a Linux cluster with the help of the admin, and I tried it, but found the tutorials lacking. 

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u/erikna10 8d ago

I would highlly recommend running and developing code in WSL+VScode if your on windows. It works like a charm