David,
Thanks for the response.
> How do you know what the MM charge sum is?
I take the point charge file generated by Sander and add up all the charges
in it. If the initial MD file is charge neutral, I am assuming the selected
subset of the MD charges should neutralize the negative charge of the QM
subsystem. If they don't, then the QM/MM system will be severely
overpolarized by the net positive charge of the total system.
> The output says that the sum of the QM charge and the MM charges is zero.
Yes, the Sander output makes that statement. However, the summation of the
point charges as described above belies that.
> Creating a minimal example that illustrates the problem would likely be a
big help.
I understand that. I will try to produce one. However, while I am doing
that, I also have to meet a deadline for generating some results on the
current system of interest. Perhaps the code used to extract the point
charges could be examined to determine if there is an error in the point
charge selection process. I can send the prmtop and coordinate (rst7) file
by email, outside the mailing list, so they won't be blocked by size
limitations. Combined and compressed they slightly exceed the size limit
accepted.
Jim
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-----Original Message-----
From: David Case <david.case.rutgers.edu>
Sent: Monday, November 18, 2019 9:25 PM
To: jimkress_58.kressworks.org; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Charge neutrality in QM/MM system
On Mon, Nov 18, 2019, James Kress wrote:
>Amber also does not create a charge neutral QM/MM system when using
>Q-Chem as the target QM application.
>QM charge is -18
>MM charge sums to +34.75201321
How do you know what the MM charge sum is? The output says that the sum of
the QM charge and the MM charges is zero.
I don't think just seeing the files you sent will allow easy progress on
figuring out what is going on. Do you see similar behavior with a small qm
region? with an uncharged QM region? Creating a minimial example that
illustrates the problem would likely be a big help.
....dac
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Received on Mon Nov 18 2019 - 21:00:02 PST
