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On the difference between additive and subtractive QM/MM calculations

Cao, Lili LU and Ryde, Ulf LU orcid (2018) In Frontiers in Chemistry 6(APR).
Abstract

The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two... (More)

The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e., the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic, and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended.

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author
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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Additive QM/MM, Electrostatic embedding, Haem oxygenase, Mechanical embedding, QM/MM, Subtractive QM/MM, Sulfite oxidase
in
Frontiers in Chemistry
volume
6
issue
APR
article number
89
publisher
Frontiers Media S. A.
external identifiers
  • scopus:85047500196
  • pmid:29666794
ISSN
2296-2646
DOI
10.3389/fchem.2018.00089
project
Computational Studies of Nitrogenase
language
English
LU publication?
yes
id
a988f0d0-703d-49db-8179-cbe12d85b142
date added to LUP
2018-06-07 09:07:59
date last changed
2024-06-24 15:30:47
@article{a988f0d0-703d-49db-8179-cbe12d85b142,
  abstract     = {{<p>The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e., the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic, and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended.</p>}},
  author       = {{Cao, Lili and Ryde, Ulf}},
  issn         = {{2296-2646}},
  keywords     = {{Additive QM/MM; Electrostatic embedding; Haem oxygenase; Mechanical embedding; QM/MM; Subtractive QM/MM; Sulfite oxidase}},
  language     = {{eng}},
  month        = {{04}},
  number       = {{APR}},
  publisher    = {{Frontiers Media S. A.}},
  series       = {{Frontiers in Chemistry}},
  title        = {{On the difference between additive and subtractive QM/MM calculations}},
  url          = {{http://dx.doi.org/10.3389/fchem.2018.00089}},
  doi          = {{10.3389/fchem.2018.00089}},
  volume       = {{6}},
  year         = {{2018}},
}