Comment by minimaltom
9 hours ago
Thank you for such a detailed explanation! I was wondering why we don't see MD everywhere and things like protein folding are all based on ML.
Is there anything like a getting-started for working with MACE or orbmol, a 'hello world'? Like maybe simulating Allolactose binding to lac1 ?
Heh. Unfortunately computer science is really the weird one out where open source is the norm. A lot of computational chemistry knowledge is mainly transferred in research labs and through college classes, and you have to pay for a lot of the tools. But hopefully I can at least point you in some useful directions. Here's a bit of an overview of the CC workflow and free options (note I haven't tried all the free options):
1. The first thing you need to do is start with some atomic structure. You can often find pre-existing pieces (through websites like pubchem), but you need to cobble them together. I use chemcraft and gaussview for this, but those are paid options. I've heard good things about the FOSS program Avogadro though.
2. Once you've built the structure of interest, you want to calculate properties of it. Note that we only infrequently simulate the atom's movement, since that's quite expensive. There's a lot of techniques that let us get the most bang for buck, like calculating transition states, or states of lowest energy which we call intermediates, or running something called an IRC, which follows the molecule to its lowest energy point (note we pretty much always think about these things in terms of energy). The traditional programs I use for this are Gaussian and ORCA (ORCA is free but you do have to create an account on their forum). Newer methods include MACE and orbmol, which are pretty much only used for trajectories (e.g. running through time) as far as I know. This newer crop of programs are much more FOSS, but they aren't as rigorous so my lab uses them only as a "rough draft". I pulled in one of my current notebooks if you're curious to try it out: https://github.com/smj-edison/qc-tools/blob/main/examples/ml...
3. Interpreting results/debugging problems. This is currently done in my workflow using a python script to extract values from the job runfiles (oh yeah, did I mention the terrible DX? A lot of this stuff is done by hand-writing a job text file and then using regex to parse the logfile). We do a lot of analysis based on relative energies (this is something called transition state theory of reactions).
I definitely glossed over a lot of details, but this is long enough as is. Definitely let me know if you have questions! If you do want a "hello world" though, I'd definitely check out the notebook I linked to. You'll have to create a file called "start.xyz" with some sort of chemistry program (or use AI to pull one for you), and then you can run the system through time. I would use a system I'm researching right now, but I'm not sure what our lab's policy is on broadcasting things to the world.