« first day (939 days earlier)   

1:42 AM
@LordStryker Haha... you know my issue with academia.se! Far too much blargh ;)
@GeoffHutchison I am truly amazed what you are trying to do. And by the likes of it, eventually succeed. Congratulations on the grant! The idea with the QR codes is just insanely awesome.
@GeoffHutchison, @LordStryker By now you know, I don't like B3LYP. And I don't like the Pople basis sets either. But I am aware that this is (unfortunately) still *the* method to do. You could set an example though ;)
On another note: Why are you using 6-31G*? Why not cc-pVDZ or def2-SVP or SDD?
 
2:11 AM
@Martin Beyond PM7, the methods are still being debated.
I was thinking of B3LYP/6-31G* simply because it's popular - to use as a baseline to show that other combinations are likely more useful and accurate in modern life.
So we do want to set a good example, but we're not sure we want to churn through all the molecules with 18 methods.
Suggestions are welcome. :-)
 
2:46 AM
@GeoffHutchison This is absolutely understandable. I would not consider this a feasible as well. My usual approach is using DF-BP86/def2-SVP for starters. It outperforms easily any other functional on the cost/accuracy level. Then apply hybrid functionals like pbe0 and later on something along the lines of M06 (but I don't really like that either). Something with dispersion is also quite nice, but I remember you were mentioning wB97xD, so you were already taking that into account.
I think wB97xD only implements the second generation of Grimme's dispersion. Maybe switch to some functional that is able to use the superior D3(BJ) version, though. B97D3 comes to mind, but this is not long range corrected though.
 
3:04 AM
 
3:42 AM
@GeoffHutchison, 2 questions, 1, it seems like my interface is missing everything shown here avogadro.cc/wiki/Tutorials:Drawing_molecules below adjust hydrogens checkbox, can I fix it? 2, is there some way to make pretty flyaround videos?
n/m I found display settings and animation trajectory, now I just need fragments library, sorry for the static
 
 
1 hour later…
5:05 AM
@JoeStavitsky No worries. One of my plans for the next term is to hire some undergrads to update the documentation, particularly with newer screenshots
The fragment library is under Build -> Insert -> Fragment
@Martin There are plenty of other open questions.. ECP for metals, solvation, etc. But one of the goals of John Pople was to have a "model chemistry" database like this. Let people explore and compare.
 
 
10 hours later…
3:23 PM
@LordStryker where do you guys normally get trajectory files for animation in avolgadro?
@GeoffHutchison where do you normally get trajectory files?
 
3:39 PM
@JoeStavitsky I assume these trajectory files are coming from dynamics simulations. I don't have much experience with these at all. I deal mainly (almost exclusively) with stationary states.
 
@LordStryker, no they are just camera paths for animations. I would assume that somehow they would let me record this inside the package, but I don't see that function
@LordStryker, Its very simple, just 1 xyz coord per frame
 
@JoeStavitsky I see. Well, I still have zero experience with that and I also have little experience with Avogadro in general. Perhaps @GeoffHutchison will be able to help you out.
I'm glad to see that you're using Avogadro though :)
 
@LordStryker, a simple program for a simple person :)
 

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