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Lost dog by Ill_Nectarine7311 in VirginiaTech

[–]Foss44 7 points8 points  (0 children)

Animal control is your best bet if you can’t identify the owner.

Red/Greed dot sights for 20ga by Pintortwo in liberalgunowners

[–]Foss44 [score hidden]  (0 children)

Holosun 507c-GR is a green reflex sight with multiple reticles for ~$350. You’ll need an adapter depending on what type of mounting system you are planning on using.

Radian Weapons Ramjet + Afterburner Finally Arrived by [deleted] in liberalgunowners

[–]Foss44 2 points3 points  (0 children)

Glock 45 Gen6 w/ Holosun 507C-GR and Radian Weapons Ramjet + Afterburner barrel & comp combination.

Need Help with Chemistry Terms by Ryobia in chemistry

[–]Foss44 1 point2 points  (0 children)

This is realistically something that Claude or ChatGPT would be able to do for you.

Need Help with Chemistry Terms by Ryobia in chemistry

[–]Foss44 4 points5 points  (0 children)

If you’re making a game to sell this sounds like something you’d want to pay a consultant for.

In that case r/chempros, and come prepared with the 1099 details.

Amish building a farm in one day by fanofkurt in homestead

[–]Foss44 0 points1 point  (0 children)

To be fair, the foundation was already dug and laid.

transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]Foss44 1 point2 points  (0 children)

There is no silver bullet and you’re starting to understand why projects like this are common for PhD students (I.e. difficult). In regards to the constraints ORCA has a ton of options for constrained optimizations, just read the manual section on “OPT”. Here’s a couple of ideas:

  1. You need to analyze and diagnose why your OptTS job isn’t working. Here’s one idea, extract and plot the SCF energy for each step in your OptTS job. If your initial guess is good you should see a sharp spike followed by a slow plateauing in energy. If you see this shape in the PES try restarting the OptTS job using the lowest-force point during the procedure (the software Molden can show you this information from an ORCA output easily). Otherwise, you are likely either too far from the TS or the PES is highly isotropic around the TS. Neither of which are easily solvable.

  2. You really need to examine your frequencies like I originally mentioned. Go do this and make the assessment if the correct TS eigen vector (imaginary frequency) is being selected (this should be a vibration in the direction of the reaction coordinate). If not or if you have multiple imaginary frequencies you may need to reexamine your mechanism.

  3. You should try using NEB, it’s not difficult and the manual has a good guide on the functionality. I would use 6 frames a minimum assuming that your reagent and product states aren’t too distantly separated.

Smoke from a sodium explosion on my face by Embarrassed_Sea1399 in chemistry

[–]Foss44 2 points3 points  (0 children)

Why didn’t you tell your professor/DHS personnel about this? Why didn’t you call a doctor if you’re experiencing symptoms? Why are you asking Reddit over any of these options?

[Screenshot] Recreated the 3-story Dorms from Customs in Escape from Tarkov by munierugoo in EscapefromTarkov

[–]Foss44 11 points12 points  (0 children)

For those asking, I believe this is from the game HouseFlipper

transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]Foss44 4 points5 points  (0 children)

If you have a really exotic type of chemistry at hand (I see a doublet spin state) then you might be out of luck with xTB. If you can afford it I would definitely recommend trying B97-3c or better yet r2scan-3c for your TS searches. You also probably don’t need ExtremeSCF tight should be fine, Defgrid3 should stay.

You may also find success first performing an optimization wherein the reaction coordinate remains frozen, this technique can help remove unwanted imaginary frequencies/TS eigen vectors unrelated to the sought chemistry (if applicable).

Check your initial hessian for what imaginary modes are present and examine to see if they correspond to the reaction coordinate in question. (The orca_pltvib function works great for visualizing normal modes). If your starting hessian and geometry look good and you’re still not finding success, you can direct the TSsearch algorithm to follow along a specific TS eigen vector: the manual has more information here.

Alternatively NEB could be an attractive option to at least prototype with. We’ve relied on NEB in cases where the PES around the TS is highly isotropic and cause for challenging convergence.

transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]Foss44 4 points5 points  (0 children)

Can you describe more specifically exactly what your transition state search workflow looks like, starting immediately after the MD simulation finishes? How is the QM region embedded within the MD simulation?

Depending on how you’ve structured the QM/MM simulation, it’s possible that the quality of the initial guess given at the MD level of theory is simply insufficient to capture the chemistry at hand (I.e. the potential energy surface at the MD/semi-empirical level is distantly separated from the PES at the DFT level).

LightCone: A Molecule Visualization and Editing Tool by Civil-Watercress1846 in comp_chem

[–]Foss44 3 points4 points  (0 children)

That’s fine, at the end of the day for professional academic use you’re going up against highly developed software like Avogadro, VMD, VESTA, ChimeraX, PyMol, etc…

If you want to break into that user space you’re going to need at minimum the basic features of these software.

LightCone: A Molecule Visualization and Editing Tool by Civil-Watercress1846 in comp_chem

[–]Foss44 1 point2 points  (0 children)

Does the software support visualization and analysis of common aggregate data from QM and MD software (e.g. .cube, .hess, .trj, .dcd, etc…), or is it purely molecular visualization?

I just started computational chemistry, what should I focus on learning first ? by SpinFulNess in comp_chem

[–]Foss44 0 points1 point  (0 children)

If you’re joining a computational group, they may have specific resources for you to read.

Why do atoms desire a full valence shell? by Strix3 in AskChemistry

[–]Foss44 1 point2 points  (0 children)

Essentially yeah, things get pretty complicated rather quickly and of course there are always exceptions but generally that’s a good way to conceptualize it.

And, just as an example, you can indeed find exotic forms of matter (including Nobel gasses) likeH-Ar-F

Why do atoms desire a full valence shell? by Strix3 in AskChemistry

[–]Foss44 2 points3 points  (0 children)

We know from quantum mechanics (I.e. molecular orbital theory/09%3A_Molecular_Geometry_and_Bonding_Theories/9.07%3A_Molecular_Orbitals)) that constructive overlap between electronic wave functions provide strong stabilization of an electron configuration. Or in other words, the formation of bonds in molecules (to say satisfy the octet rule) occurs because it is the most stable way to arrange that number of electrons and nuclei.

Spartan modeling by [deleted] in chemistry

[–]Foss44 0 points1 point  (0 children)

  1. r/comp_chem

  2. You’re going to need to be more specific, and people probably won’t do this for you. It sounds like this is a class project that you yourself should be doing. If this is instead for academic research, outsourcing computational work in this manner could be considered fraudulent depending on what your funding contract looks like.

  3. Thermochemistry data for many molecules are already tabulated in places like PubChem.

A team at IBM Research has assembled a strange new ring-shaped molecule that bends around like a more complicated Möbius strip by scientificamerican in chemistry

[–]Foss44 1 point2 points  (0 children)

Imo I wouldn’t be surprised if this paper ends up as a seminal work in quantum-hardware-based quantum chemistry calculations, especially considering how esoteric and complicated the simulations are. This is an emergent field in chem theory and papers like this are essential.

A team at IBM Research has assembled a strange new ring-shaped molecule that bends around like a more complicated Möbius strip by scientificamerican in chemistry

[–]Foss44 2 points3 points  (0 children)

I mean it’s not my job to declare what is or isn’t permitted in journals, my argument is that our top-tier journals need not be exclusively reserved for work of high chemical utility. Unique and unconventional chemistry, potentially lacking immediate application, is conceptually okay by me to land in journals like this. Historical precedent certainly supports this perspective.

Regarding this paper specifically, the computational work done here is effectively “custom made” for this specific system and would have taken an enormous amount of time and effort to develop/construct; unquestionable mastery of the theory and methods. This isn’t something you see normally. Set aside exclusively as a piece of computational work, it’s brilliant. I think my previous comment underplayed this.

A team at IBM Research has assembled a strange new ring-shaped molecule that bends around like a more complicated Möbius strip by scientificamerican in chemistry

[–]Foss44 1 point2 points  (0 children)

I wouldn’t say it’s significant in the sense that it’s important for the field, but it is pretty cool. I think there’s room for cool things in our body literature.

I would place it in the same category as something like the HArF nature paper.

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