On the difference between additive and subtractive QM/MM calculations
Cao, Lili LU and Ryde, Ulf LU
(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.
(Less)
- author
- Cao, Lili
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2018-04-01
- 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
- 2024-07-23 18:27:13
@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}},
}