Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator

Yu, Tang; Alejandre, José; López-Rendón, Roberto; Martyna, Glenn; Tuckerman, Mark E.

doi:10.1016/j.chemphys.2010.02.014

Cited by 58 publications

(41 citation statements)

References 43 publications

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“…The equations of motions were integrated using a measure-preserving integrator for MD in the isothermal -isobaric ensemble. [283,284] Figure 10 shows that both methods give statistically identical results (see Table S5 of the Supporting Information available via the article webpage).…”

Section: Validating Npt Simulationsmentioning

confidence: 58%

On the inner workings of Monte Carlo codes

Dubbeldam

Torres‐Knoop

Walton

2013

Molecular Simulation

375

398

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We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as zeolites and metal -organic frameworks. Conventional MC is discussed and compared to advanced techniques such as reactive MC, configurational-bias Monte Carlo and continuous fractional MC. The latter technique overcomes the problem of low insertion probabilities in open systems. Other modern methods are (hyper-)parallel tempering, Wang-Landau sampling and nested sampling. Details on the techniques and acceptance rules as well as to what systems these techniques can be applied are provided. We highlight consistency tests to help validate and debug MC codes.

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Section: Validating Npt Simulationsmentioning

confidence: 58%

On the inner workings of Monte Carlo codes

Dubbeldam

Torres‐Knoop

Walton

2013

Molecular Simulation

375

398

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“…Thermo-and barostats can be combined with the Miller scheme to control the temperature and pressure. [68,70,71] Figure 9 shows that this type of scheme has excellent energy conservation over many nanoseconds. The CO 2 is modelled as rigid and integrated using the quaternion integration scheme of Miller et al [67].…”

Section: For a Single Adsorbed Component The Transport Diffusion Coementioning

confidence: 99%

RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

Dubbeldam

Calero

Ellis

et al. 2015

Molecular Simulation

1,569

1,529

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A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self-and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.

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“…This then requires great care in the construction of partition functions with different independent variables as indicated by Martyna and co-workers when deriving fully flexible simulation cell protocols for constant pressure simulations. 29,30 Building on the previously proposed Z NVγT employed by our research group also requires care, as different reasonable definitions of the shape transformation variable λ result in two different partition functions.…”

Section: Results For Equivalence Between MCmentioning

confidence: 99%

On the Equivalence of Schemes for Simulating Bilayers at Constant Surface Tension

Rodgers

Smit

2012

J. Chem. Theory Comput.

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Lipid bilayers are simulated using flexible simulation cells in order to allow for relaxations in area per lipid as bilayer content and temperature are varied. We develop a suite of Monte Carlo (MC) moves designed to generate constant surface tension γ and constant pressure P and find that the NPT partition function proposed by Attard [J. Chem. Phys. 1995, 103, 9884−9885] leads to an NPγT partition function with a form invariant to choice of independent shape variables. We then compare this suite of MC moves to NPγT MC moves previously employed in our group as well as a pair of MC moves designed to replicate the NP ∥ P ⊥ T "ensemble" often used in molecular dynamics simulations to yield zero surface tension and constant pressure. A detailed analysis of shape fluctuations in a small bilayer system reveals that the two latter MC move sets are different from one another as well as from our new suite of MC moves, as justified by careful analysis of the partition functions. However, the study of a larger bilayer system reveals that, for practical purposes for this system, all six MC move sets are comparable to one another.

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Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator

Cited by 58 publications

References 43 publications

On the inner workings of Monte Carlo codes

On the inner workings of Monte Carlo codes

RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

On the Equivalence of Schemes for Simulating Bilayers at Constant Surface Tension

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