Re: [AMBER] qmcut in Amber14 Manual

From: Marc van der Kamp <>
Date: Mon, 11 May 2015 09:43:32 +0100

Dear Robert,

I didn't write the manual (nor am I a developer), but here some comments
that may clarify things:

On 11 May 2015 at 07:13, Robert Molt <> wrote:

> Good morning,
> I have some confusions on the qmcut keyword. On p.138, it states, in
> describing the keyword: " By default this is the same as the value of
> cut chosen for the classical region, and the default generally does not
> need to be changed."

This is the case for when PBCs are used, I think - then one can say that
qmcut doesn't have to be changed from the classical cut-off.

> On p.149, it states:
> " A cutoff is applied to QM/MM interactions in QM/MM simulations using
> electrostatic embedding with and without PBCs. This leads to
> discontinuities in the potential energy surface and poor energy
> conservation. In the case of QM/MM simulations without PBCs, this cutoff
> (qmcut variable in the &qmmm namelist) can be set to a number that is
> larger than the simulated system, thus effectively not applying a
> cutoff. This is recommended."
> I thus infer that this addendum is an exception to the rule of thumb on
> p.138.

Note "In the case of QM/MM simulations without PBCs" here.

> However, this leads to a confusion for me.
> 1.) The note is in reference to usage of Gaussian as a QM software. The
> second quote above would be seemingly true of ANY software (if you have
> a cutoff without a switching function, there will be a discontinuity).
> Am I mistaken?
> Yes, it would be the case for any software, as well as Amber's built in
(sqm) semi-empirical methods.
But if you have PBCs with PME, this will work for QM/MM as well.

> 2.) I am confused about setting qmcut to a number larger than the
> simulated system. Doesn't this result in a "QM region + cutoff larger
> than box" error, inherently?
I suppose it would (easy to test if you're curious), but ONLY if you
enforce PBCs, in which case you wouldn't really need to set qmcut to a
large number.

Hope this helps,

> --
> Dr. Robert Molt Jr.
> Nigel Richards Research Group
> Department of Chemistry & Chemical Biology
> Indiana University-Purdue University Indianapolis
> LD 326
> 402 N. Blackford St.
> Indianapolis, IN 46202
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Received on Mon May 11 2015 - 02:00:03 PDT
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