Statistical mechanics of Hamiltonian adaptive resolution simulations

Español, Pep; Delgado‐Buscalioni, Rafael; Everaers, Ralf; Potestio, Raffaello; Donadio, Davide; Kremer, Kurt

doi:10.1063/1.4907006

Cited by 52 publications

(93 citation statements)

References 25 publications

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“…This in turn led the adaptive idea to be conceptually forced in a canonical or microcanonical ensemble only for the sake of familiarity with standard MD approaches. A global Hamiltonian does not make the conceptual derivation more rigorous than a forced-based approach, in fact it leads to implicit violations of basic principles of statistical mechanics and/or an increase in computational costs (i.e., lack of energy conservation [25,34], thermodynamic state-dependent Hamiltonians employed for first principles statistical mechanics analysis [35], increase in number of interactions as a function of the size of the system which makes the number of calculations impossible even for futuristic computers [27]). It is our opinion that the essential point is that the change of resolution is not a realistic physical process thus there is not a physics of reference against which to compare the correctness of properties of molecules with hybrid resolution.…”

Section: Grand Canonical-like Adaptive Resolution Simulation (Gc-adrementioning

confidence: 99%

Molecular dynamics in a grand ensemble: Bergmann–Lebowitz model and adaptive resolution simulation

et al. 2015

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This article deals with the molecular dynamics simulation of open systems that can exchange energy and matter with a reservoir; the physics of the reservoir and its interactions with the system are described by the model introduced by Bergmann and Lebowitz (P G Bergmann and J L Lebowitz 1955 Phys. Rev. 99 578). Despite its conceptual appeal, the model did not gain popularity in the field of molecular simulation and, as a consequence, did not play a role in the development of open system molecular simulation techniques, even though it can provide the conceptual legitimation of simulation techniques that mimic open systems. We shall demonstrate that the model can serve as a tool in devising both numerical procedures and conceptual definitions of physical quantities that cannot be defined in a straightforward way by systems with a fixed number of molecules. In particular, we discuss the utility of the Bergmann-Lebowitz (BL) model for the calculation of equilibrium time correlation functions within the grand canonical adaptive resolution method (GC-AdResS) and report numerical results for the case of liquid water.

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Section: Grand Canonical-like Adaptive Resolution Simulation (Gc-adrementioning

confidence: 99%

Molecular dynamics in a grand ensemble: Bergmann–Lebowitz model and adaptive resolution simulation

et al. 2015

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“…Only recently it became feasible to set up an all-atom MD simulation for a larger set of DNA molecules [51,53] characterized by a single packing geometry with only a partial characterization of the DNA countercharge and solvent ordering. This approach has been later extended by the applications of the multiscale MD technique AdResS (Adaptive Resolution Scheme) [54][55][56][57][58][59][60][61][62][63][64][65][66][67], which has been already successfully applied to various biological systems [68][69][70][71][72][73][74][75][76][77], enabling a concurrent and consistent coupling between the atomistic (AT) and the coarse-grained (CG) representations with a key feature of allowing molecules to freely move not only in real space but also in the resolution space across different regions and change their resolution on the fly according to their position in the computational domain.…”

Section: Simulating Dna Arraysmentioning

confidence: 99%

Molecular Dynamics Simulation of High Density DNA Arrays

2018

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Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine) counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities.

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“…This approach complements the work of Kreis et al, which does not have a conserved Hamiltonian. Their method could presumably be incorporated with the Hamiltonian-based version of AdRes, [34][35][36][37] in which case This formalism allows us to connect the equilibrium properties of the high resolution region to those expected from a simulation performed in full detail. We build on previous work, 16 where we derived adaptive boundaries specifically for a mixed explicit-continuum model with a spherical domain.…”

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Communication: Adaptive boundaries in multiscale simulations

Wagoner

Pande

2018

The Journal of Chemical Physics

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Combined-resolution simulations are an effective way to study molecular properties across a range of length and time scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of degrees of freedom required to accurately represent even a simple molecular process can vary by several orders of magnitude throughout the course of a simulation, and adaptive boundaries react to these changes to include an appropriate but not excessive amount of detail. Here, we derive the Hamiltonian and distribution function for such a molecular simulation. We also design an algorithm that can efficiently sample the boundary as a new coordinate of the system. We apply this framework to a mixed explicit/continuum simulation of a peptide in solvent. We use this example to discuss the conditions necessary for a successful implementation of adaptive boundaries that is both efficient and accurate in reproducing molecular properties. Published by AIP Publishing. https://doi.org/10.1063/1.5025826Multiscale models are an effective way to simulate molecular systems. The motivation is clear: a high-resolution model can capture physical detail, while a low-resolution model offers computational efficiency and is sometimes better suited or more easily parameterized for large-scale phenomena. 1 There are two strategies for multiscale modeling. In the first, multiple independent simulations are used for different levels of resolution. Combined intelligently, the sum is worth more than the parts: simulations at one level motivate and parameterize simulations at another. [2][3][4] The focus of this work is the second approach, which combines multiple levels of resolution into a single simulation. These simulations use a fine-grained (FG) model for a region of interest and a computationally efficient coarse-grained (CG) model elsewhere. Examples include mixed quantum and molecular mechanical, 5,6 mixed all-atom and coarse grained (CG), 7-13 and hybrid explicit-continuum solvent models. [14][15][16][17][18][19][20][21] Accurately modeling the boundary between high-and low-resolution regions is the crux of a combined-resolution simulation. Even for a homogeneous system like bulk solvent, equilibrium properties emerge from a delicate balance of interactions with the surrounding medium. An improper handling of the boundary will break the natural symmetry, and the resulting structural artifacts can extend well beyond the boundary into other regions of the simulation. 15 We have developed a hybrid explicit-continuum solvent model that includes a boundary region over which molecules gradually, rather than abruptly, change resolution. This boundary method avoids the structural artifacts common to hybrid solvent models and accurately reproduces thermodynamic properties throughout the entire explicit domain. 15,16 This boundary method is similar to that introduced in the Adaptive Resolution (AdRes) approach, 22,23 a method used to couple high r...

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Statistical mechanics of Hamiltonian adaptive resolution simulations

Cited by 52 publications

References 25 publications

Molecular dynamics in a grand ensemble: Bergmann–Lebowitz model and adaptive resolution simulation

Molecular dynamics in a grand ensemble: Bergmann–Lebowitz model and adaptive resolution simulation

Molecular Dynamics Simulation of High Density DNA Arrays

Communication: Adaptive boundaries in multiscale simulations

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