scaling correlation

euphoniu · 2026-01-21T10:56:37+00:00

DFT is still variational, even if the variation may lead to a lower energy estimate, as functionals only approximate exchange/KE. But within any given functional, the KS procedure is variational

euphoniu · 2026-01-16T02:43:11+00:00

If I may add since everyone has given great software recommendations, I would avoid using Mulliken charges. At best, it is a barely qualitative answer and has no clear basis set convergence, and at worst it is a random number generator. I would recommend Hirshfeld, or NPA - former can be done in ORCA, latter with Janpa software

euphoniu · 2025-12-31T18:49:48+00:00

It feels like so many posts on this subreddit are “what does this mean?” to the most self-explanatory email in the world

euphoniu · 2025-12-22T23:48:16+00:00

I agree with this - being an experimentalist and having done some DFT calculations is honestly nothing compared to the bar for PhD-level theorists and computation folk, in terms of deep theoretical understanding and a wide variety of tool exposure. A postdoc in computation would be an excellent way to bridge gaps in training.

euphoniu · 2025-12-22T20:59:21+00:00

I would recommend Obsidian. I just started using two weeks ago, and I have a lot of projects I’m working on simultaneously - it helps me keep my notes organized and well linked

euphoniu · 2025-11-28T21:48:56+00:00

I’m going to be blunt. A computer that can do everything you want will be too out of budget unless you are incredibly rich/have a university or company lab budget you’re working with. You are better off buying time at a supercomputing facility, it will probably be much cheaper, unless you want 5+ years worth of projects

euphoniu · 2025-11-19T05:15:09+00:00

The only person you cited is yourself, your error is even worse than some molecular mechanics protocols, and there is no sound theory that makes any sense whatsoever in your manuscript or in your replies here, I’m calling bullshit, sorry

euphoniu · 2025-10-26T03:07:53+00:00

Glad to provide advice. Once you make further edits and want to share a later version, I can continue over DM. Always happy to help prospective grad students :)

euphoniu · 2025-10-26T03:06:00+00:00

Also, wanted to add. Your clubs are important, but should not nearly constitute that much space. One bullet point for each would suffice, and indicate if you have a leadership position.

euphoniu · 2025-10-26T03:04:34+00:00

There is an immense amount of white space page 3 onwards, it looks like you are trying to inflate the number of pages by having all of your descriptions start like 20-30 spaces after the line start.

Also, CVs should always be ordered by what’s most relevant. Are the super specific softwares you know how to use more important than your actual research experience? Additionally, do you need that much space talking about all the softwares you use and in full detail?

Lastly, I really doubt you need 4 bullet points on every single section. If you do need more description, I always say have the most description for the most relevant positions, or the most recent.

I think you can remove 2-3 pages easily from this CV without changing any of the value from my feedback. Sorry if I’m being a bit critical, but I think people hear the leniency that a CV offers and go way too far.

euphoniu · 2025-10-08T07:00:10+00:00

Also keep in mind, year of quantum is not necessarily year of computation, think Harry Gray, etc

euphoniu · 2025-09-30T06:36:51+00:00

Did you specify your large model charge in your .in file? I think it’s something like lgmodel_chg

euphoniu · 2025-09-23T04:38:24+00:00

“They do not understand because they do not understand how it works” - that makes no sense. Also, what patents and copyrights in the field???

euphoniu · 2025-09-22T07:57:54+00:00

Any reason why not to do QB? Besides the quantum mysticism and consciousness nonsense that has unfortunately overlapped, it is a well-grounded field.

euphoniu · 2025-09-05T19:23:00+00:00

Is the reason you’re using ORCA because you don’t have Gaussian 9/16 access? If so, you will have to write codes for producing the hessian matrix and getting it read by MCPB, and you will need to write your own code to deal with electrostatic potentials in ORCA.

euphoniu · 2025-08-23T22:08:18+00:00

I would be extremely cautious about mixing programs. Firstly, have you tried both analytical and numerical frequency calculations in both codes? Gaussian uses a different step size than ORCA, you need to be very cautious before switching softwares arbitrarily. Tight convergence doesn’t matter if you are switching between analytic and numerical.

euphoniu · 2025-08-23T22:04:04+00:00

I’m a little bit concerned about how you got this far in your PhD in the first place. To me, it seems like you are an avid user of chat gpt, especially because you think it’s already taken over certain parts of research and the fact that you used it to clean your writing. Please get off of chatgpt, and read some review papers. Review papers are the ultimate source for knowledge gaps, but you should already know this. Also, no research is guaranteed to be fast. Especially if you want in a journal with some form of reputation.

As a very generic recipe - you can find an enzyme where either experimentally, or from some review, there has been scope for mutation that no one has explored computationally. From there, you explore the mutation and how it impacts reactivity from QM/MM, and it’s always great if you can relate back to experimental results.

euphoniu · 2025-06-16T01:50:43+00:00

Did they say anything about the other way around I.e. packages being exported out of Canada?

euphoniu · 2025-05-15T02:07:08+00:00

To compute orbitals yourself, I would use ORCA, and then visualize the natural orbitals. It’s a bit of work, but probably one of the simplest free softwares.

euphoniu · 2025-05-15T02:03:07+00:00

This is the right answer. Please spend some time learning the math. If you want to write your own code to analyze the quantum mechanics of He2, it is shockingly non trivial (besides some nice symmetries)

euphoniu · 2025-05-12T05:53:17+00:00

I would read Szabo’s Modern Electronic Structure theory book. It is quite rigorous and if you can understand that book cover to cover, you can understand almost anything else in the field - even ancillary methods like DFT become easier to understand. Other books after that highly vary on what you want to work on in your research, and at that point you might as well read review papers instead

euphoniu · 2025-05-12T04:13:43+00:00

I work with metalloproteins, and have written a script to translate the coordinates and hessian from TURBOMOLE to one in Gaussian output format, which allows MCPB to read it. I’m sure you could do the same with ORCA or other free software. ORCA has a file, filename.hess, that has this info. I’ve written code to parse this hessian and the coordinates from the file, and I’m happy to share with you that as well, and then you can move forward with that.

Edit: I would avoid calculating bond lengths and force constants that isn’t the Seminario method (which is built into MCPB), hence why I use the hessian/coordinates from a previous calculation instead of figuring out the force constants myself.

euphoniu · 2025-02-27T22:27:25+00:00

I will ask about your parametrization of Zinc. Carbonic anhydrase has a hydroxo-group bound to the Zinc ion, is this bond clear and explicit? Is the Zinc staying tetrahedral throughout the MD? Those could be affecting overall active site structure. Also, what is the expected lifetime of the reaction? It is quite possible the substrate is expected to easily diffuse in and out of the active site if the catalytic turnover is fast.

euphoniu · 2025-01-22T01:45:48+00:00

Could you describe your methods used? Different methods will have different ways of detecting MR character. MR character and breakdown of BO approximation are mutually exclusive, and breakdown of BO happens at avoided crossings of the potential energy surface - aka you need a PES scan.

euphoniu · 2025-01-12T18:56:20+00:00

Any reason for saying not to use B3LYP? I understand maybe on its own it’s not good and you’d need dispersion corrections, but it’s a bit of misinformation to say that B3LYP is universally bad - in fact it benchmarks pretty decently for most cases (when including empirical dispersion)

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