Hierarchical Modeling of Polystyrene: From Atomistic to Coarse-Grained Simulations

Harmandaris, Vagelis; Adhikari, Narayan Prasad; Vegt, Nico F. A. van der; Kremer, Kurt

doi:10.1021/ma0606399

Cited by 331 publications

(485 citation statements)

References 37 publications

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“…The clustering is even more pronounced in the FM system due to lower solvation free energy of AA butane in CG butane than in itself (Table 1). The clustering effect can be quantified with preferential solvation parameters d i that we calculate by integrating g i,j (r) using eqn (12). In Table 2 the preferential solvation results are summarized.…”

Section: Preferential Solvation In Mixed Aa/cg Butanementioning

confidence: 99%

“…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%

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

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

186

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: Preferential Solvation In Mixed Aa/cg Butanementioning

confidence: 99%

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.

186

198

View full text Add to dashboard Cite

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“…On the contrary, the DBI correlation-based approach, that is based on the decomposition of the CG potential in bonded and non-bonded components, can be a computationally efficient alternative. Such a methodology neglects many body terms; however, for several systems can provide an accurate prediction of the structural and thermodynamic properties [20,21,22,23].…”

Section: Discussionmentioning

confidence: 99%

From Atomistic to Systematic Coarse-Grained Models for Molecular Systems

Harmandaris¹,

Kalligiannaki²,

Katsoulakis³

et al. 2017

Proceedings of the 2nd International Conference on Uncertainty Quantification in Computational Sciences and Engineering (UNCECO

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Abstract. The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

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“…In order to evaluate the effect of the relaxation at large distances, the internal distances between pairs of repeat units separated by L repeat units 57 Figure 10b, which compares the frequency of the internal distances for L= 5, 10 and 50 calculated using the generated and MD relaxed microstructures.…”

Section: Structural Propertiesmentioning

confidence: 99%

Atomistic simulations of the structure of highly crosslinked sulfonated poly(styrene-co-divinylbenzene) ion exchange resins

et al. 2015

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The microscopic structure of highly crosslinked sulfonated poly(styrene-codivinylbenze) resins have been modeled by generating atomistic microstructures using stochastic-like algorithms that are , subsequently, relaxed using molecular dynamics.Two different generation algorithms have been tested. Relaxation of the microstructures generated by the first algorithm, which is based on a homogeneous construction of the resin, leads to a significant overestimation of the experimental density as well as to an unsatisfactory description of the porosity. In contrast, the generation approach that combines algorithms for the heterogeneous growing and branching of the chains enables the formation of crosslinks with different topologies. In particular, the intrinsic heterogeneity observed in these resins is well reproduced when topological loops, which are defined by two or more crosslinks closing a cycle, are present in their microscopic description. Thus, the apparent density, porosity and pore volume estimated using microstructures with these topological loops, called super-crosslinks, are in very good agreement with experimental measures. Although the backbone dihedral angle distribution of the generated and relaxed models is not influenced by the topology, the number and type of crosslinks affect the medium-and long-range atomic disposition of the backbone atoms and the distribution of the sulfonic groups. Analysis of the distribution of the local density indicates that super-crosslinks are responsible of the heterogeneous homogenization observed during the MD relaxation. Finally, - stacking interactions between aromatic phenyl groups have been analyzed, those in which the two rings adopt a T-shaped disposition being considerably more abundant than those with the rings co-facially oriented, independently of the resin topology.3

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Hierarchical Modeling of Polystyrene: From Atomistic to Coarse-Grained Simulations

Cited by 331 publications

References 37 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

From Atomistic to Systematic Coarse-Grained Models for Molecular Systems

Atomistic simulations of the structure of highly crosslinked sulfonated poly(styrene-co-divinylbenzene) ion exchange resins

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