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A comparison of barostats for the mechanical characterization of metal-organic frameworks

Sven Rogge UGent, Louis Vanduyfhuys UGent, An Ghysels UGent, Michel Waroquier UGent, Toon Verstraelen UGent, G Maurin and Veronique Van Speybroeck UGent (2015) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 11(12). p.5583-5597
abstract
In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, are critically compared to characterize closed pore the rigid MOF-5 and flexible MIL-53(Al) metal organic frameworks. We investigate the performance of the three barostats, the Berendsen, the Martyna-Tuckerman-Tobias-Klein (MTTK), and the Langevin coupling methods, in reproducing the cell parameters and the pressure versus volume behavior in isothermal isobaric simulations. A thermodynamic integration method is used to construct the free energy profiles as a function of volume at finite temperature. It is observed that the aforementioned static properties are well-reproduced with the three barostats. However, for static properties depending nonlinearly on the pressure, the Berendsen barostat might give deviating results as it suppresses pressure fluctuations more drastically. Finally, dynamic properties, which are directly related to the fluctuations of the cell, such as the time to transition from the large-pore to the closed-pore phase, cannot be well-reproduced by any of the coupling schemes.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MOLECULAR-DYNAMICS SIMULATIONS, ELASTIC NEUTRON-SCATTERING, STATISTICAL-MECHANICS, COORDINATION POLYMERS, CANONICAL ENSEMBLE, COMPUTATIONAL EXPLORATION, STRUCTURAL TRANSITIONS, FLEXIBLE MIL-53(CR), INFORMATION-THEORY, ISORETICULAR MOFS
journal title
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
J. Chem. Theory Comput.
volume
11
issue
12
pages
5583 - 5597
Web of Science type
Article
Web of Science id
000366223400004
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
5.301 (2015)
JCR rank
5/35 (2015)
JCR quartile
1 (2015)
ISSN
1549-9618
DOI
10.1021/acs.jctc.5b00748
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
7024350
handle
http://hdl.handle.net/1854/LU-7024350
date created
2016-01-05 09:16:09
date last changed
2017-04-18 10:54:33
@article{7024350,
  abstract     = {In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, are critically compared to characterize closed pore the rigid MOF-5 and flexible MIL-53(Al) metal organic frameworks. We investigate the performance of the three barostats, the Berendsen, the Martyna-Tuckerman-Tobias-Klein (MTTK), and the Langevin coupling methods, in reproducing the cell parameters and the pressure versus volume behavior in isothermal isobaric simulations. A thermodynamic integration method is used to construct the free energy profiles as a function of volume at finite temperature. It is observed that the aforementioned static properties are well-reproduced with the three barostats. However, for static properties depending nonlinearly on the pressure, the Berendsen barostat might give deviating results as it suppresses pressure fluctuations more drastically. Finally, dynamic properties, which are directly related to the fluctuations of the cell, such as the time to transition from the large-pore to the closed-pore phase, cannot be well-reproduced by any of the coupling schemes.},
  author       = {Rogge, Sven and Vanduyfhuys, Louis and Ghysels, An and Waroquier, Michel and Verstraelen, Toon and Maurin, G and Van Speybroeck, Veronique},
  issn         = {1549-9618},
  journal      = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
  keyword      = {MOLECULAR-DYNAMICS SIMULATIONS,ELASTIC NEUTRON-SCATTERING,STATISTICAL-MECHANICS,COORDINATION POLYMERS,CANONICAL ENSEMBLE,COMPUTATIONAL EXPLORATION,STRUCTURAL TRANSITIONS,FLEXIBLE MIL-53(CR),INFORMATION-THEORY,ISORETICULAR MOFS},
  language     = {eng},
  number       = {12},
  pages        = {5583--5597},
  title        = {A comparison of barostats for the mechanical characterization of metal-organic frameworks},
  url          = {http://dx.doi.org/10.1021/acs.jctc.5b00748},
  volume       = {11},
  year         = {2015},
}

Chicago
Rogge, Sven, Louis Vanduyfhuys, An Ghysels, Michel Waroquier, Toon Verstraelen, G Maurin, and Veronique Van Speybroeck. 2015. “A Comparison of Barostats for the Mechanical Characterization of Metal-organic Frameworks.” Journal of Chemical Theory and Computation 11 (12): 5583–5597.
APA
Rogge, S., Vanduyfhuys, L., Ghysels, A., Waroquier, M., Verstraelen, T., Maurin, G., & Van Speybroeck, V. (2015). A comparison of barostats for the mechanical characterization of metal-organic frameworks. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11(12), 5583–5597.
Vancouver
1.
Rogge S, Vanduyfhuys L, Ghysels A, Waroquier M, Verstraelen T, Maurin G, et al. A comparison of barostats for the mechanical characterization of metal-organic frameworks. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2015;11(12):5583–97.
MLA
Rogge, Sven, Louis Vanduyfhuys, An Ghysels, et al. “A Comparison of Barostats for the Mechanical Characterization of Metal-organic Frameworks.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11.12 (2015): 5583–5597. Print.