Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate

Hess, Berk; León, Salvador; Vegt, Nico F. A. van der; Kremer, Kurt

doi:10.1039/b602076c

Cited by 128 publications

(133 citation statements)

References 15 publications

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“…Indeed, several of such hybrid schemes have recently been proposed, falling into four classes: back-mapping methods, interface methods, ''constant l'' techniques and fixed resolution methods. Back mapping methods [9][10][11][12][13][14][15][16][17] allow switching between the different levels of resolution, i.e. reconstruct the atomistic structural ensemble that underlies a CG representation for interesting configurations.…”

Section: Introductionmentioning

confidence: 99%

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

191

198

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Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1 : 1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein, together with the solvent, is coarse-grained.

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Section: Introductionmentioning

confidence: 99%

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

191

198

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“…We refer to the process of mapping atomistic coordinates into a coarse-grained model as "finegraining", which is has found extensive use in the investigation of complex proteins [66][67][68], as well as other molecular systems [69][70][71][72][73]. Here, we use fine-graining to inform electronic property calculations, which complement the aforementioned structural analysis.…”

Section: Fine-grainingmentioning

confidence: 99%

“…This mapping is constrained so the center-of-mass of the group of atoms is identical to the center-of-mass of the coarse-grained site. Subsequent relaxation of bonded constriants is required for each molecule to find a realistic atomistic morphology [69,71], unless an internal coordiante system is maintained to permit constrains such as the expected tor-sional rotation of a thiophene ring or a phenyl group [70,80] to be enforced during fine-graining. In some cases, it can be useful to treat each group as a rigid body, keeping constant the relative positions and orientations of atoms within the group according to a geometrically-relaxed template [81,82].…”

Section: Fine-grainingmentioning

confidence: 99%

“…The atomic positions are therefore adjusted to make the conformation of the molecule more realistic, by energetically relaxing the molecules over very short timescales. This can be performed on a molecule-by-molecule basis in isolation [67,68], or in situ using energetic minimization methodologies [69][70][71], or even full molecular dynamics simulations [72]. In some cases, particularly when polymer chains with high conformational disorder are being simulated, it is useful to apply additional geometrical constraints during the fine-graining process to maintain the original centers-of-mass of each group according to the fully equilibrated, corasegrained morphology generation.…”

Section: Fine-grainingmentioning

confidence: 99%

“…Such constraints can also help to simulate non-equilibrium effects such as a significant shear force [83]. A final relaxation stage is frequently performed with a longer molecular dynamics simulation, in order to fully relax the chains in the simulation volume and ensure that there are no atomic overlaps between molecules [69][70][71][72]. When a physically realistic, atomistic conformation for the molecule has been achieved, it can be used by QCCs to determine the electronic structure.…”

Section: Fine-grainingmentioning

confidence: 99%

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Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology

Jones

Jankowski

2017

Molecular Simulation

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Rationally designing roll-to-roll printed organic photovoltaics requires a fundamental understanding of active layer morphologies optimized for charge separation and transport, and which ingredients can be used to self-assemble those morphologies. In this review article we discuss advances in three areas of computational modeling that provide insight into active layer morphology and the charge transport properties that result. We explain the computational bottlenecks prohibiting atomistically-detailed simulations of device-scale active layers and the coarse-graining and hardware acceleration strategies for overcoming them. We review coarse-grained simulations of organic photovoltaic active layers and show that high throughput simulations of experimentally-relevant length scales are now accessible. We describe a new Python package diffractometer that permits grazing-incidence X-ray scattering patterns of simulated active layers to be compared against experiments. We explain the accurate calculation of charge-carrier mobilities from coarse-grained active layer morphologies by using atomistic backmapping, quantum chemical calculations, and kinetic Monte Carlo simulations. We employ these simulations to show that ordering of poly(3-hexylthiophene-2,5-diyl) explains a factor of 1000 improvement in charge mobility. In concert, we present a suite of computational tools enabling large-scale electronic properties of organic photovoltaics to be studied and screened for by molecular simulations.

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Gas Transport in Dense Polymeric Membranes, Molecular Dynamics Simulations

Neyertz

2013

Encyclopedia of Membrane Science and Technology

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Classical simulations such as molecular dynamics (MD) are powerful tools to either complement experimental evidence or to predict gas transport properties in polymers. They can reproduce the gas uptake curves and characterize at the molecular level both the mechanisms of gas mobility and the structural and dynamical changes of the matrices. It is also possible to evaluate the gas diffusion and solubility coefficients, thus leading to model permeabilities. However, realistic fully atomistic simulations are currently restricted to the 10 −9 to 10 −7 s timescale, which is hardly compatible with the longer relaxations of high molecular weight polymers and the establishment of the Fickian diffusion regime for slowly diffusing gases. Consequently, pure MD will often have to be coupled with other simulation techniques in order to overcome these shortcomings, both during the model preparation procedures and the analyses of gas transport.

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Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate

Cited by 128 publications

References 15 publications

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology

Gas Transport in Dense Polymeric Membranes, Molecular Dynamics Simulations

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