On the Convergence of QM/MM Energies
Hu, LiHong LU ; Soederhjelm, Paer and Ryde, Ulf LU
(2011)
In Journal of Chemical Theory and Computation
7(3).
p.761-777
- Abstract
- We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a second-sphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as a reference. We have tested 12 different ways to redistribute charges close to the junctions (to avoid overpolarization of the QM system), but once the junctions are moved away from the active site, there is little need to redistribute the charges. We have tested 13 different variants of QM/MM approaches, including two schemes to correct errors caused by the truncation of the QM system. However, we see little gain from such correction schemes; on... (More)
- We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a second-sphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as a reference. We have tested 12 different ways to redistribute charges close to the junctions (to avoid overpolarization of the QM system), but once the junctions are moved away from the active site, there is little need to redistribute the charges. We have tested 13 different variants of QM/MM approaches, including two schemes to correct errors caused by the truncation of the QM system. However, we see little gain from such correction schemes; on the contrary, they are sensitive to the charge-redistribution scheme and may cause large errors if charges are close to the junctions. In fact, the best results were obtained with a mechanical embedding approach that does not employ any correction scheme and ignores polarization. It gives a mean unsigned error for 40 QM systems of different sizes of 7 kJ/mol with a maximum error of 28 kJ/mol. The errors can be significantly decreased if bonds between the QM and MM system (junctions) are moved one residue away from all active-site residues. Then, most QM/MM variants give mean unsigned errors of 5-9 kJ/mol, maximum errors of 16-35 kJ/mol, and only five to seven residues give an error of over 5 kJ/mol. In general, QM/MM calculations converge faster with system size than pure QM calculations. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1869254
- author
- Hu, LiHong
LU
; Soederhjelm, Paer
and Ryde, Ulf
LU
- organization
- publishing date
- 2011
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Theory and Computation
- volume
- 7
- issue
- 3
- pages
- 761 - 777
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- wos:000287991300025
- scopus:79952607247
- pmid:26596307
- ISSN
- 1549-9618
- DOI
- 10.1021/ct100530r
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
- id
- 653ce692-ca87-4454-be0b-01f5cd52e008 (old id 1869254)
- date added to LUP
- 2016-04-01 10:10:35
- date last changed
- 2023-01-02 01:51:48
@article{653ce692-ca87-4454-be0b-01f5cd52e008,
abstract = {{We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a second-sphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as a reference. We have tested 12 different ways to redistribute charges close to the junctions (to avoid overpolarization of the QM system), but once the junctions are moved away from the active site, there is little need to redistribute the charges. We have tested 13 different variants of QM/MM approaches, including two schemes to correct errors caused by the truncation of the QM system. However, we see little gain from such correction schemes; on the contrary, they are sensitive to the charge-redistribution scheme and may cause large errors if charges are close to the junctions. In fact, the best results were obtained with a mechanical embedding approach that does not employ any correction scheme and ignores polarization. It gives a mean unsigned error for 40 QM systems of different sizes of 7 kJ/mol with a maximum error of 28 kJ/mol. The errors can be significantly decreased if bonds between the QM and MM system (junctions) are moved one residue away from all active-site residues. Then, most QM/MM variants give mean unsigned errors of 5-9 kJ/mol, maximum errors of 16-35 kJ/mol, and only five to seven residues give an error of over 5 kJ/mol. In general, QM/MM calculations converge faster with system size than pure QM calculations.}},
author = {{Hu, LiHong and Soederhjelm, Paer and Ryde, Ulf}},
issn = {{1549-9618}},
language = {{eng}},
number = {{3}},
pages = {{761--777}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Journal of Chemical Theory and Computation}},
title = {{On the Convergence of QM/MM Energies}},
url = {{https://lup.lub.lu.se/search/files/1627070/2338974.pdf}},
doi = {{10.1021/ct100530r}},
volume = {{7}},
year = {{2011}},
}