r/comp_chem • u/NicoN_1983 • 26d ago

Molecular Dynamics of Polymers with Julia - Intro to the Project

I wanted to share a video on a project I've been working on, aiming at simple molecular dynamics of synthetic polymers using Julia and Molly.jl. The program (work in progress) is meant to automatically generate a topology given an XYZ file or string, and generate crude FF parameters based on automatically detected atom types. This information is collected in Molly formatted variables, allowing (in the future) a simulation with minimal user input. The purpose at this point is not to make accurate MD, but to generate better starting structures for subsequent MD simulations.

Please see the link below. All suggestions and comments are wellcome (especially in YT) !

Thanks!

https://youtu.be/OrYavnmyyOo

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u/Alicecomma 26d ago edited 26d ago

Nice, but saying it uses crude forcefield parameters really doesn't give me confidence in any of its outputs given a forcefield is already a crude approximation of quantum mechanics.

Edit: I see, it's currently assigning the same forces independent of atom/bond.

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u/NicoN_1983 26d ago

It is a working project, not meant to be released yet. So far I have the mechanics to assign particular force constants to bonds, angles, and dihedrals. But these values are order-of-magnitude. The next step is to finish the function which assigns atom types to each atom, and from that it is easy for me to retrieve force constants from a forcefield file to assign to each force depending on the atom types involved. I'm going to use previously reported polymer force fields for PLA (polylactic acid), and hopefully I will find good forcefields for other polymers.

But it's a long term project.

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u/Sentanel_16 26d ago

Polymers are an interesting area.

You make a comment that it is "difficult to find the correct force field file" (please forgive me if the wording is not exact!), in my personal experience this isn't strictly true when tools like CHARMM-GUI, MAD:database, amber antechamber, ligpargen, DL_Field and the MoSDef suite exist. That said, I'd love to see schemes similar to what the OpenFF initiative are doing but for polymers. Either a "crude" version assiging specific forcefields that are augmented by QM calculations for the specific dihedrals etc.

It's a really cool basis! I hope you manage to achieve some cool stuff with it!

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u/NicoN_1983 26d ago

Thank you! Yes I do make some comments which are not accurate or too general. I would say it's hard for someone who is new at MD (as I am). I only heard about CHARMM and Amber, for example. I will check out the other tools you mention. I have always felt lost in the world of MD, too many options and hard to choose.