From adaptive resolution to molecular dynamics of open systems

Cortes-Huerto, Robinson; Praprotnik, Matej; Kremer, Kurt; Site, Luigi Delle

doi:10.1140/epjb/s10051-021-00193-w

Cited by 18 publications

(14 citation statements)

References 130 publications

(195 reference statements)

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“…[36]). For example, the long lasting question on whether a global Hamiltonian with physical meaning can be written [37] was no more an issue [10] . The one‐body thermodynamic force in Δ is now recast into a one‐body potential:

φ (x) = - \int_{x_{0}}^{x} {\vec{F}}_{t h} (x^{'}) \cdot {\vec{e}}_{x} normald x^{'}

with x 0 the position of the AT/Δ interface and the resulting total interaction potential of this set up reads:

true U_{tot} = U_{tot}^{AT} + \sum_{k \in Δ \cup TR} φ ((), X_{k})

…”

Section: Methodologiesmentioning

confidence: 99%

“…For example, the long lasting question on whether a global Hamiltonian with physical meaning can be written [37] was no more an issue. [10] The one-body thermodynamic force in Δ is now recast into a one-body potential:…”

Section: Chemistryopenmentioning

confidence: 99%

“…Recently developed numerical techniques based on spatial adaptive molecular resolution (AdResS)[ 5 , 6 , 7 , 8 , 9 ] have allowed for the simulation of small open subsystems that exchange molecules with a larger coarse‐grained environment. [10] This progress paves the way towards simulations of small systems at high resolution embedded in a simplified environment. The results for structural and thermodynamic properties have the same accuracy of calculations at high resolution for large systems.…”

Section: Introductionmentioning

confidence: 97%

“…It captures relevant quantum characteristics of the hydrogen bond formation by describing the spatial delocalization in space of a light atom as the hydrogen and its effects on the structural and dynamical properties of the bonding network; yet, the cost of simulations is still very high compared to classical simulations. Recently developed numerical techniques based on spatial adaptive molecular resolution (AdResS) [5–9] have allowed for the simulation of small open subsystems that exchange molecules with a larger coarse‐grained environment [10] . This progress paves the way towards simulations of small systems at high resolution embedded in a simplified environment.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Path Integral Molecular Dynamics of Liquid Water in a Mean‐Field Particle Reservoir

2022

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We present a simulation scheme for path integral simulation of molecular liquids where a small open region is embedded in a large reservoir of non interacting point‐particles. The scheme is based on the latest development of the adaptive resolution technique AdResS and allows for the space‐dependent change of molecular resolution from a path integral representation with 120 degrees of freedom to a point particle that does not interact with other molecules and vice versa. The method is applied to liquid water and implies a sizable gain regarding the request of computational resources compared to full path integral simulations. Given the role of water as universal solvent with a specific hydrogen bonding network, the path integral treatment of water molecules is important to describe the quantum effects of hydrogen atoms’ delocalization in space on the hydrogen bonding network. The method presented here implies feasible computational efforts compared to full path integral simulations of liquid water which, on large scales, are often prohibitive.

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φ (x) = - \int_{x_{0}}^{x} {\vec{F}}_{t h} (x^{'}) \cdot {\vec{e}}_{x} normald x^{'}

with x 0 the position of the AT/Δ interface and the resulting total interaction potential of this set up reads:

true U_{tot} = U_{tot}^{AT} + \sum_{k \in Δ \cup TR} φ ((), X_{k})

…”

Section: Methodologiesmentioning

confidence: 99%

Section: Chemistryopenmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Path Integral Molecular Dynamics of Liquid Water in a Mean‐Field Particle Reservoir

2022

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“…Therefore, the overall multiresolution interaction must be considered to be renormalized at both levels, FG and CG. However, this systematic thermodynamic connection is often missing in many current multiresolution models. − For example, the AdResS treats the overall potential as where coupling parameter λ α varies from 0 to 1 to couple the FG and CG systems with their bulk (naked) interactions V α FG and V α CG , respectively. While this interpolative approach has shown to be able to capture various thermodynamic properties at equilibrium, the thermodynamic consistency principle of eq suggests that there is no formal theory to support the idea that eq can be written in terms of the “naked” FG potential as done in eq .…”

Section: Basics Of Bottom-up Coarse-grained Modelingmentioning

confidence: 99%

Bottom-up Coarse-Graining: Principles and Perspectives

Jin

Pak

Durumeric

et al. 2022

J. Chem. Theory Comput.

149

147

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Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.

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On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir

Gholami

Klein

Site

2021

Advcd Theory and Sims

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In a previous paper, a precise relation between the chemical potential of a fully atomistic simulation and the simulation of an open system in the adaptive resolution method (AdResS) was identified. The starting point was the equivalence derived from the statistical partition functions between the grand potentials, Ω, of the open system and of the equivalent subregion in the fully atomistic simulation of reference. In this work, instead, the authors treat the identity for the grand potential based on the thermodynamic relation normalΩ=−pV$\Omega =-pV$ and investigate the behavior of the pressure in the coupling region of the adaptive resolution method (AdResS). The authors confirm the physical consistency of the method for determining the chemical potential described by the previous work and strengthen it further by identifying a clear numerical relation between the potential that couples the open system to the reservoir on the one hand and the local pressure of the reference fully atomistic system on the other hand. Such a relation is of crucial importance in the perspective of coupling the AdResS method for open system to the continuum hydrodynamic regime.

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From adaptive resolution to molecular dynamics of open systems

Cited by 18 publications

References 130 publications

Path Integral Molecular Dynamics of Liquid Water in a Mean‐Field Particle Reservoir

Path Integral Molecular Dynamics of Liquid Water in a Mean‐Field Particle Reservoir

Bottom-up Coarse-Graining: Principles and Perspectives

On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir

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