[AMBER] Question about usage of external QM in QM/MM

From: Fabrício Bracht <fabracht1.gmail.com>
Date: Thu, 4 Aug 2016 14:59:10 -0300

Hello. I have a few doubts regarding the use of Gaussian to perform qm/mm.
First let say that the choice of using an external qm involves the fact the
the catalytic group is a copper complex in the triplet state, and thus, I
am not sure whether semi-empirical methods would give good reliable
results. But any comment on this would be appreciated.
My question may be a silly one, but it is regarding the use of periodic
conditions or not and the use of the large cutoff. I have performed QM/MM
simulations before but never considered the use of non periodic systems.
The amber 16 manual states that PBC are supported with extQM but that PME
is not and the use of the cutoff leads to discontinuities in the energy
surface. So the manual advises you to use non-periodic simulations. Well,
I do not understand why that is a better choice. From what I understood,
the use of a non periodic system means that there is no imaging and thus,
every molecule that hits the border interacts with the border. Wouldn't
this affect the energy conservation more than the discontinuity caused by
the large cutoff in a periodic system?
Do you have any recommendation as to how to setup the system. A have the
structure from a very long classic MD simulation solvated in a cubic box.
Thank you
Fabrício Bracht
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Received on Thu Aug 04 2016 - 11:00:03 PDT
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