[AMBER] about adding counter ions

From: B. Bowie <brendabowie0103.gmail.com>
Date: Mon, 29 Jul 2013 00:44:15 -0400

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.
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Received on Sun Jul 28 2013 - 22:00:02 PDT
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