QM/MM simulation of liquid water with an adaptive quantum region

Research output: Contribution to journalArticle

Standard

QM/MM simulation of liquid water with an adaptive quantum region. / Bernstein, Noam; Varnai, Csilla; Solt, Iván; Winfield, Steven A; Payne, Mike C; Simon, István; Fuxreiter, Mónika; Csányi, Gábor.

In: Physical Chemistry Chemical Physics, 2012.

Research output: Contribution to journalArticle

Harvard

Bernstein, N, Varnai, C, Solt, I, Winfield, SA, Payne, MC, Simon, I, Fuxreiter, M & Csányi, G 2012, 'QM/MM simulation of liquid water with an adaptive quantum region', Physical Chemistry Chemical Physics. https://doi.org/10.1039/c1cp22600b

APA

Bernstein, N., Varnai, C., Solt, I., Winfield, S. A., Payne, M. C., Simon, I., Fuxreiter, M., & Csányi, G. (2012). QM/MM simulation of liquid water with an adaptive quantum region. Physical Chemistry Chemical Physics. https://doi.org/10.1039/c1cp22600b

Vancouver

Author

Bernstein, Noam ; Varnai, Csilla ; Solt, Iván ; Winfield, Steven A ; Payne, Mike C ; Simon, István ; Fuxreiter, Mónika ; Csányi, Gábor. / QM/MM simulation of liquid water with an adaptive quantum region. In: Physical Chemistry Chemical Physics. 2012.

Bibtex

@article{c707ea828b694cd1bc51d8cf31e69f77,
title = "QM/MM simulation of liquid water with an adaptive quantum region",
abstract = "The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 {\AA}) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl− ion.",
author = "Noam Bernstein and Csilla Varnai and Iv{\'a}n Solt and Winfield, {Steven A} and Payne, {Mike C} and Istv{\'a}n Simon and M{\'o}nika Fuxreiter and G{\'a}bor Cs{\'a}nyi",
year = "2012",
doi = "10.1039/c1cp22600b",
language = "English",
journal = "Physical Chemistry Chemical Physics",
issn = "1463-9076",
publisher = "Royal Society of Chemistry",

}

RIS

TY - JOUR

T1 - QM/MM simulation of liquid water with an adaptive quantum region

AU - Bernstein, Noam

AU - Varnai, Csilla

AU - Solt, Iván

AU - Winfield, Steven A

AU - Payne, Mike C

AU - Simon, István

AU - Fuxreiter, Mónika

AU - Csányi, Gábor

PY - 2012

Y1 - 2012

N2 - The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl− ion.

AB - The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl− ion.

UR - http://dx.doi.org/10.1039/c1cp22600b

U2 - 10.1039/c1cp22600b

DO - 10.1039/c1cp22600b

M3 - Article

JO - Physical Chemistry Chemical Physics

JF - Physical Chemistry Chemical Physics

SN - 1463-9076

ER -