Re: [AMBER] QM/MM dynamics: metal oxides

From: emanuele <>
Date: Sun, 27 Jan 2019 11:43:17 +0000

Hey David,

First of all thank to all you guys for doing a great job with main-list.

1. Thanks for the hint. As matter of fact, when it comes to look up to
the only solute structure I could even not include the Li ions into the
QM region, however,  I was also interested to understand the ion-pairing
phenomena between solute (metal oxides) and Li ions: closed-pair,
semi-closed, and etc. Normally, I do this analysis by looking at radial
distribution function (RDF).

If Li ions are not included in QM part, as you said, they just move away
from the solute molecules- I haven't still figured out why.

So, I wonder if there is a way to account correctly Li's influence on
the solute molecules at QM/MM level?

As always, thanks for the help.



Il 26/01/2019 15:18, David Case ha scritto:
> On Fri, Jan 25, 2019, emanuele falbo wrote:
>> Sorry , I meant that the dynamics fails when the M solute molecule and 15
>> Li ions are both treated with semi-empirical PM6, whereas the water at MM
>> level .
> First: there is (I think) no reason to treat Li+ ions as quantum
> mechanical. Are you expecting any electron transfer from the metal?
> Second: there is a good reason not to do this: the QM/MM code is
> designed for a compact QM region. As I understand it, your Li ions may
> move all over the place.
> Finally: you are correct in noting that SCF failures can be hard to fix,
> especially with a highly negative charge. The Reference Manual has some
> suggestions of things to try. But handling metal oxides (as opposed to
> organic molecules) may require considerable experimentation.
> ...good luck...dac
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Received on Sun Jan 27 2019 - 04:00:02 PST
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