[AMBER] qmcut in Amber14 Manual

From: Robert Molt <rwmolt07.gmail.com>
Date: Mon, 11 May 2015 02:13:18 -0400

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."

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

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?

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?

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 Sun May 10 2015 - 23:30:02 PDT
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