I'm trying to learn how to use GAMESS. I used Avogadro to download the structure of tricalcium bis(phosphate), then I accidentally ran a runtyp=energy on the structure and it succeeded, so I assumed the resulting structure is better than what avogadro got and used that one instead.

I don't even know if geometry optimization is the first thing I should do. Maybe I should use another runtyp first and then optimize the result?

Maybe the fact that it's a salt is what's getting in the way? Maybe I have to specify the charges of the cations and anions somewhere.

Maybe I have to preoptimize it in Avogadro, because I don't think the straight line of 3 Ca followed by 2 $PO_4$ perfectly aligned remotely resembles what $Ca_3(PO_4)_2$ looks like. (save the pastebin as .log and open it in avogadro so you'll see how it is structured)

Here's a pastebin of the result. The input is printed in the begining, I took off the extended credits section on the begining.



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    $\begingroup$ Why would you want to optimize a non-existent molecule in the first place? $\endgroup$ – Ivan Neretin Jul 29 '16 at 7:37
  • $\begingroup$ en.wikipedia.org/wiki/Tricalcium_phosphate $\endgroup$ – FinnTheHuman Jul 29 '16 at 7:39
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    $\begingroup$ You seem to think that all existing compounds are made of molecules. This is very much not so. The compound $\ce{Ca3(PO4)2}$ does exist, of course, but there is no such molecule. $\endgroup$ – Ivan Neretin Jul 29 '16 at 7:44
  • $\begingroup$ Can you clarify what do you mean by that? Geometry optimization is only supposed to be done on molecules, is that it? Like I said, I'm learning. I'm not a chemist, My knowledge of chemistry is bellow amateur level. $\endgroup$ – FinnTheHuman Jul 29 '16 at 7:58
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    $\begingroup$ You really need a more thorough understanding of chemistry first, then you need some decent understanding in quantum mechanics, because you need to combine that to run meaningful computations. Try optimising simple organic molecules first. Use something like water, ammonia, hydrogen chloride, methane, ethane, etc. These have already quite a lot of pitfalls to start with. Obviously you can optimise the geometry of $\ce{Ca3(PO4)2}$, but how meaningful is that as a molecule in the gas phase? $\endgroup$ – Martin - マーチン Jul 29 '16 at 8:45

I'm trying to learn how to use GAMESS.

I'm not a chemist, my knowledge of chemistry is below amateur level.

There is a serious contradiction out there: quantum chemistry is way above amateur level. Unlike playing computer games, quantum chemistry can not be done in a just-get-in-and-drive way. You need a serious theoretical background to make meaningful calculations.

Thus, for instance, you have to understand that usually by default all the calculations in quantum chemical programs are done for an isolated molecule in gas phase. Doing geometry optimization for ionic compound in such settings is, well, let's say, it is not so meaningful. Very likely, you want to do something totally different, say, establish the crystal structure of solid $\ce{Ca3(PO4)2}$, but that is a totally different task. In fact, you do even need a special program (like CRYSTAL) to achieve that.

  • $\begingroup$ What I really want is to build a "good enough" computational approximation of reaction rate, equilibrium constant and activation energy for any given reaction. I'm making a Minecraft mod, and I wanted it to be realistic and educational. So after building a good enough model that would work for at least big set of reactions then I would come up with more practical questions, like how to separate this product frome this solution, etc. $\endgroup$ – FinnTheHuman Jul 29 '16 at 9:17
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    $\begingroup$ @FinnTheHuman, well, then I strongly advice you to stop wasting your time, since building such an approximation is currently beyond the dreams of chemists. $\endgroup$ – Wildcat Jul 29 '16 at 9:20
  • $\begingroup$ Thank you, I didn't know that. Can you give me advise on one or more really large databases where this kind of data was obtained experimentally? NIST is really disappointing on that matter. Do you know about any other? $\endgroup$ – FinnTheHuman Jul 29 '16 at 10:06

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