Automated analysis and benchmarking of GCMC simulation programs in application to gas adsorption

Gowers, Richard; Farmahini, Amir Hajiahmadi; Friedrich, Daniel; Sarkisov, Lev

doi:10.1080/08927022.2017.1375492

Cited by 35 publications

(31 citation statements)

References 55 publications

(60 reference statements)

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“…Both these packages have been developed by CCP Forge, and they are available free of charge. DL_Monte has been shown to have a computational performance that is comparable to several other Monte Carlo codes [39]. Besides, having commonalities with DL_Poly, it was a natural choice to complement the MD simulations carried out using DL_Poly.…”

Section: Methodsmentioning

confidence: 99%

Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

2018

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Silicalite is an important nanoporous material that finds applications in several industries, including gas separation and catalysis. While the sorption, structure, and dynamics of several molecules confined in the pores of silicalite have been reported, most of these studies have been restricted to low pressures. Here we report a comparative study of sorption, structure, and dynamics of CO2 and ethane in silicalite at high pressures (up to 100 bar) using a combination of Monte Carlo (MC) and molecular dynamics (MD) simulations. The behavior of the two fluids is studied in terms of the simulated sorption isotherms, the positional and orientational distribution of sorbed molecules in silicalite, and their translational diffusion, vibrational spectra, and rotational motion. Both CO2 and ethane are found to exhibit orientational ordering in silicalite pores; however, at high pressures, while CO2 prefers to reside in the channel intersections, ethane molecules reside mostly in the sinusoidal channels. While CO2 exhibits a higher self-diffusion coefficient than ethane at low pressures, at high pressures, it becomes slower than ethane. Both CO2 and ethane exhibit rotational motion at two time scales. At both time scales, the rotational motion of ethane is faster. The differences observed here in the behavior of CO2 and ethane in silicalite pores can be seen as a consequence of an interplay of the kinetic diameter of the two molecules and the quadrupole moment of CO2.

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Section: Methodsmentioning

confidence: 99%

Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

2018

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“…We refer readers to discussions elsewhere on this topic, for example, Refs. [12, 43–45]. In typical situations, N max can be set to any value greater than τ , since in principle C j = 0 for all j > τ .…”

Section: Computing Error In Specific Observablesmentioning

confidence: 99%

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]

et al. 2019

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The quantitative assessment of uncertainty and sampling quality is essential in molecular simulation. Many systems of interest are highly complex, often at the edge of current computational capabilities. Modelers must therefore analyze and communicate statistical uncertainties so that “consumers” of simulated data understand its significance and limitations. This article covers key analyses appropriate for trajectory data generated by conventional simulation methods such as molecular dynamics and (single Markov chain) Monte Carlo. It also provides guidance for analyzing some ‘enhanced’ sampling approaches. We do not discuss systematic errors arising, e.g., from inaccuracy in the chosen model or force field.

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“…After all simulations have finished, we sort the materials by the desired property obtained by the simulation and, voilá, shortlist the top few for experimental testing 4 . This is the obvious value of high-throughput computational screenings, and it is predicated on sufficiently accurate molecular models and simulations (i.e., sufficient sampling [86, 87]) to rank the materials by their desired adsorption property with high statistical confidence.…”

Section: Molecular Models and Methodsmentioning

confidence: 99%

The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation

Sturluson

Huynh

Kaija

et al. 2019

Molecular Simulation

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Metal-organic frameworks (MOFs) are highly tuneable, extended-network, crystalline, nanoporous materials with applications in gas storage, separations, and sensing. We review how molecular models and simulations of gas adsorption in MOFs have informed the discovery of performant MOFs for methane, hydrogen, and oxygen storage, xenon, carbon dioxide, and chemical warfare agent capture, and xylene enrichment. Particularly, we highlight how large, open databases of MOF crystal structures, post-processed to enable molecular simulations, are a platform for computational materials discovery. We discuss how to orient research efforts to routinise the computational discovery of MOFs for adsorption-based engineering applications.

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Automated analysis and benchmarking of GCMC simulation programs in application to gas adsorption

Cited by 35 publications

References 55 publications

Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]

The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation

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