Molecular Dynamics of Fluids: The Gaussian Overlap Model II

Kabadi, Vinayak N.

doi:10.1002/bbpc.19860900403

Cited by 18 publications

(5 citation statements)

References 13 publications

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“…Moreover, the calculation of forces and torques is strongly simplified. Specifically, we consider a modification of the original GB model which was introduced by Kabadi 46 . The modification involves a coefficient d w which acts as a factor on the well width of the original GB potential.…”

Section: Parametrization In Terms Of a Gay-berne Potentialmentioning

confidence: 99%

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Angle-resolved effective potentials for disk-shaped molecules

Heinemann

Pałczynski

Dzubiella

et al. 2014

The Journal of Chemical Physics

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We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van-der-Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

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Section: Parametrization In Terms Of a Gay-berne Potentialmentioning

confidence: 99%

“…For comparison we now introduce two further models, K1 and K2. These are parametrizations of the Kabadi potential 46 , which only differs from the Gay-Berne potential through the distance-dependent part in Eq. (23).…”

Section: B Kabadi Models (K1 and K2)mentioning

confidence: 99%

Angle-resolved effective potentials for disk-shaped molecules

Heinemann

Pałczynski

Dzubiella

et al. 2014

The Journal of Chemical Physics

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“…The strength parameter determines the interaction strength for different orientations and consists of two parameters ϵ 0 and ϵ F ϵ S , which refer to the well-depth of cross configuration and the ratio between the well-depth of the face-to-face configuration ϵ F and that of the side-to-side configuration ϵ S , respectively . The term d w is introduced to control the “softness” of the potential . Therefore, there are in total five parameters to fully specify the GB potential.…”

Section: Anisotropic Dpd Formulationmentioning

confidence: 99%

A Mori–Zwanzig Dissipative Particle Dynamics Approach for Anisotropic Coarse Grained Molecular Dynamics

Chan

Wenzel

2023

J. Chem. Theory Comput.

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Coarse grained (CG) molecular dynamics simulations are widely used to accelerate atomistic simulations but generally lack a formalism to preserve the dynamics of the system. For spherical particles, the Mori−Zwanzig approach, while computationally complex, has ameliorated this problem. Here we present an anisotropic dissipative particle dynamics (ADPD) model as an extension of this approach, which accounts for the anisotropy for both conservative and nonconservative interactions. For a simple anisotropic system we parametrize the coarse grained force field representing ellipsoidal CG particles from the fullatomistic simulation. To represent the anisotropy of the system, both the conservative and dissipative terms are approximated using the Gay− Berne (GB) functional forms via a force-matching approach. We compare our model with other CG models and demonstrate that it yields better results in both static and dynamical properties. The inclusion of the anisotropic nonconservative force preserves the microscopic dynamical details, and hence the dynamical properties, such as diffusivity, can be better reproduced by the aspherical model. By generalizing the isotropic DPD model, this framework is effective and promising for the development of the CG model for polymers, macromolecules, and biological systems.

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“…( 3)] with new parameters chosen to match the "direct" potential [Eq. (18)] for different angular arrangements. This computationally more simple approach is aimed at correctly describing the direct potential in the near field.…”

Section: Charged Ring Approachmentioning

confidence: 99%

“…Corresponding examples are the Gaussian-overlap 16 or the Gay-Berne potential 17 as well as their derivatives. 1,18,19 Even more complexity can be reached by considering many (instead of one central) interaction sites. 20,21 Further, the treatment of electrostatics can be realized through an electric multipole attached to the interaction site in a centered 2,7,9 or off-centered 22,23 arrangement.…”

Section: Introductionmentioning

confidence: 99%

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

Heinemann

Pałczynski

Dzubiella

et al. 2015

The Journal of Chemical Physics

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In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

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Molecular Dynamics of Fluids: The Gaussian Overlap Model II

Cited by 18 publications

References 13 publications

Angle-resolved effective potentials for disk-shaped molecules

Angle-resolved effective potentials for disk-shaped molecules

A Mori–Zwanzig Dissipative Particle Dynamics Approach for Anisotropic Coarse Grained Molecular Dynamics

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

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