Total charge of the system for auto opt and MD

General Discussion
1

Is there a way to set the charge (and multiplicity, for semi-empirical methods) of the system to be used by the internal optimizer and MD simulations? If not, maybe some input boxes with this info in the “Draw” panel would be helpful.

Thanks!

2

“Molecular Properties” for example. The formal charge can also be set on specific atoms using the template tool.

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Great! I did not realize the table Molecular Properties table was editable. It worked.

I was indeed able to simulate the nucleophilic attack of OH- to CH3Cl at GFN2 level with the “Dynamics” tool. That’s impressive what Avogadro2 can do now! I was just not able to make drawn bonds form and break on the dynamically along the run, but Ctrl+shift+B followed by Ctrl+B did the trick

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Yeah, I’ll have to think about this. I was showing a student something similar - if you’re using GFN-FF or GFN2 and pull on a hydrogen, the carbon will go to a sp2-radical geometry. But of course the visual bond is still there.

I think the latency of bond perception might be too high, but maybe there’s a way I can put that into a separate thread since we all have multi-core systems these days.

I’ll add that to the “videos needed” list. :slight_smile:

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