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

From: Fabrício Bracht <>
Date: Thu, 4 Aug 2016 16:29:35 -0300

Hello Andreas. Thank you for the reply. So, setting ntb = 0 and a qmcut =
999 for example would be fine? Also, I was using iwrap in my MD
simulations, and so, can I use the restart file produced at the end of the
MD or do I need to generate another one with cpptraj and reimage it?
Thank you

2016-08-04 16:17 GMT-03:00 Dr. Andreas W. Goetz <>:

> Dear Fabricio,
> Regarding triplet states: sqm (the semiempirical QM and DFTB
> implementation in Amber) at present can only handle closed shell systems.
> For open-shell systems you would need to use an external QM program,
> irrespective of the QM model that you plan to use.
> Let me clarify QM/MM with external QM programs and PBC: PME is used for
> all MM particles but not for any electrostatic interactions with the QM
> region. Thus, if you use electronic embedding (which is default), only MM
> charges within the cutoff (qmcut) are included in the QM Hamiltonian. The
> QM region does not interact with particles beyond that cutoff. MM particles
> beyond this cutoff will see a vacuum bubble instead of QM atoms. This means
> that the electric field experienced by the QM region due its surrounding
> changes abruptly whenever MM particles enter/leave the cutoff region.
> Equivalent for MM particles entering/leaving the QM cutoff, leading to
> discontinuities in the energy surface.
> The problem is less pronounced if you increase the QM/MM cutoff (qmcut).
> While it is not ideal, you are probably fine if you use a sufficiently
> large cutoff and thermostat.
> If you use a non-periodic system with solvent shell and cutoff (MM and
> QM/MM) that is larger than your system, then all electrostatic interactions
> are included and there are no discontinuities. Amber employs a soft
> half-harmonic potential at the boundary to avoid solvent evaporation (no
> hard wall) so energy is conserved. There is a limit to the pair list size
> in sander, which prevents such calculations for larger systems. One thing
> to note is that the computational cost for the MM portion of the
> calculation can become significant for very large systems in combination
> with a small QM region and/or fast QM method/implementation.
> All the best,
> Andy
> —
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email:
> Web:
> > On Aug 4, 2016, at 10:59 AM, Fabrício Bracht <>
> wrote:
> >
> > 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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> >
> >
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Received on Thu Aug 04 2016 - 12:30:03 PDT
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