From: Gerard Rowe (GerardR_at_usca.edu)
Date: Mon Mar 25 2019 - 09:52:18 CDT
If your metal ion is definitely undergoing redox change, that's going to be very difficult to treat with QM/MM unless you have also included the redox partner in the QM region. Even then, it's going to be problematic because the spin state of your resulting system is unlikely to be reasonable. This is especially true if your final system is supposed to have unpaired electrons in different regions that aren't in communication anymore. What kind of system are you studying?
I can imagine two scenarios where this will work out:
1. Your Fe(II) state is low-spin d6 (singlet) and the redox partner is a doublet. In the product state, The Fe(III) is a low-spin doublet and the redox partner is now a singlet.
2. Your Fe(II) state is high-spin d6 (sextet) and the redox partner is a singlet. In the product state, The Fe(III) is a high-spin quintet and the redox partner is now a doublet.
If scenario 1 applies, you're in luck, and the spin system will be reasonable. If it's scenario 2, you're going to run into serious issues unless the redox partner happens to be bound to the metal. Long-range separation of unpaired spin in a DFT calculation often leads to problems and non-physical solutions. You can check the spin density of your resulting wavefunction in a similar way that you can visualize molecular orbitals.
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Francesco Pietra <chiendarret_at_gmail.com>
Sent: Monday, March 25, 2019 3:16 AM
Subject: namd-l: About changing charge/multiplicity during QM-MM
I dare posing a general question on QM-MM, surely a naive question to those experienced with QM-MM (I am doing such simulations for the first time).
I am observing a change in my metalloprotein system where apparently the iron ions become bounded to other ligands, changing from FeII to FeIII. The overall charge/multiplicity is not maintained, as far as I can understand. Nonetheless, ORCA is repeating its SCF cycles, converging after a number of cycles. I have already restarted the simulation six times for 24hr on 36 cores with the same settings, in particular as to the charge and multiplicity, and the structure of the complex is no more changing, as far as it can be judged from geometry. I can't figure out how the system readjusts itself so that the QM calculation can go on.
Thanks for any comment
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