Re: [AMBER] about adding counter ions

From: David A Case <>
Date: Mon, 29 Jul 2013 07:48:47 -0400

On Mon, Jul 29, 2013, B. Bowie wrote:

> I am new in doing QM/MM simulation. I am doing an acid-catalysed
> simulation. I saw in the literature people always reported to add counter
> ions to neutralize system charges instead of using H+ or H3O+. I tried to
> add some counter ions like Cl- in QM region, but it seems the counter ions
> cannot be stabilized themselves, i.e. it forms HCl quickly. So I wonder if
> we really need to add counter ions in the system to neutralize charges. If
> so, what would be the right way to add the counter ions? Hope someone can
> give me some directions. Thanks in advance.

I don't think it is possible to give much advice without more information.
Generally, though, "diffuse" counterions would be added to the MM portion of
the simulation, not the QM part. A chloride ion would need to have its
associated water molecules to be stable as part of the QM region. If you add
"some" Cl- ions to the QM region (or anything else for that matter), without
careful attention to how they are placed, you are likely to get very bad

In most cases, you should equilibrate one state with MM alone, before
attempting to start a QM/MM calculation.

...good luck....dac

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Received on Mon Jul 29 2013 - 05:00:04 PDT
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