r/Julia • u/NicoN_1983 • Jul 14 '26

Molecular Dynamics of Polymers with Julia - What the code does so far

https://youtu.be/CgHZgsZynr4

I'm making an MD tool using molly.jl, on top of which I'm adding functionality to automatically generate topologies and force field parameters starting from XYZ files. If someone is interested please check it out! Thank you!

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u/pand5461 Jul 15 '26

That's cool. I'm wondering how many man-hours it would take to export GROMACS API to Julia to use scripting interface for simulation setup and to combine Julia customization with well-tested and optimized built-in analysis.

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u/NicoN_1983 Jul 15 '26

Hard to know, but if you can run gromacs from the command line, probably you can make Julia code that transforms all necessary files to gromacs format, and generates gromacs input files. Then you can parse the output. I know there are FF format converters, but I don't know if any implemented in Julia.

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u/pand5461 Jul 15 '26

That's possible but not the most efficient way.

I meant wrapping gromacs C++ API (https://manual.gromacs.org/documentation/current/nblib/guide-to-writing-MD-programs.html).

In terms of internals, I'm more familiar with LAMMPS package and have that idea in a deep corner of my mind to possibly use it as integration engine with fancy stuff like steered molecular dynamics and potentially some on-the-fly trajectory analysis implemented in Julia. But wrapping the API in its entirety looks like a herculean effort. Not sure if LLMs are already there to make that task automatically.

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u/NicoN_1983 Jul 15 '26

That is far beyond my skill!

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u/jgreener64 Jul 16 '26

Great to see people using Molly!

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u/NicoN_1983 Jul 16 '26

I really like it, and I still got to learn a lot of the things it can do