Deriving effective mesoscale potentials from atomistic simulations

Reith, Dirk; Pütz, Mathias; Müller‐Plathe, Florian

doi:10.1002/jcc.10307

Cited by 1,182 publications

(1,560 citation statements)

References 34 publications

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“…However, in practice the convergence is difficult to achieve and varies for different parts of the potential. 39,48 Especially attractive parts require an extensive number of iterations whereas repulsive parts converge relatively fast. Nevertheless, g ref (r) is reproduced with a good accuracy already after a small number of iterations.…”

Section: Coarse Grained Potentialsmentioning

confidence: 99%

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

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

190

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: Coarse Grained Potentialsmentioning

confidence: 99%

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

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

190

198

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“…3 It is motivated by Henderson's theorem 11 which states that there is a unique mapping between the radial distribution function (g(r)) and the intermolecular potential (V) for simple pairwise additive and spherically symmetric potentials at a given thermodynamic state point: 12 = − V k T g r ln( ( )) B (1) eq 1 is actually a potential of mean force and it equals the potential energy only in the limit of infinite dilution. 10 According to Chan et al 12 this is only valid for particles or molecules with a single interaction site rather than molecules with multiple interaction sites (like polymers) since the relation does not account for orientation correlations. However, this does not prohibit its use in the iteration algorithm (see eq 5) for the coarse-graining of polymeric systems with IBI, as the algorithm just serves as a numerical path among many possible ones that yield one effective CG potential by satisfying the condition that the trial CG potential converges when the corresponding conformational distribution matches the reference distribution in the atomistic simulations 12 and no uniqueness is assumed.…”

Section: Introductionmentioning

confidence: 99%

Modeling of Polystyrene under Confinement: Exploring the Limits of Iterative Boltzmann Inversion

Bayramoglu

Faller

2013

Macromolecules

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ABSTRACT:We explore the limits of a purely structure based coarse-graining technique, the iterative Boltzmann inversion (IBI), in the coarse-graining of a confined concentrated polystyrene solution. In the first place, some technical considerations and challenges encountered in the course of the optimization process are represented. The concepts of the choice of the initial potentials and the cross-dependency of the interactions as well as the order of optimization are discussed in detail. Furthermore, the transferability of a previously developed CG confined polystyrene solution model, the "parent CG confined model", to different degrees of confinement at constant concentration and temperature is examined. We investigate if a CG force field developed for a confined polymer solution by IBI is sensitive to changes in the degree of localization or arrangement of polymers near the surfaces although the concentration is kept constant. For this purpose, reference atomistic simulations on systems of different confinement levels have been performed. The differences in the structure and dynamics of the chains are addressed. Results are compared with those of an unconfined (bulk) system at the same concentration. The chain dimensions and orientations as a function of the distance from the surfaces are also reported. To the best of our knowledge, this is the first computational study that investigates the structural behavior of polymers in close proximity of the surfaces in a concentrated polymer solution rather than in a melt. Transferability of the parent CG confined model is tested by employing the parent force field in CG simulations of the reference systems. Results indicate that the degree of arrangement of monomers and solvent molecules near the surfaces is an important factor that needs to be paid attention to when considering the application of a CG force field developed by IBI to different degrees of confinement.

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“…The DBI, IBI and IMC methods use the pair correlation function g (2) (Q) and the assumption that the interactions depend only on the distance R between particles, that is g (2) (Q) =:ḡ(R). Thus the CG effective interaction is given bȳ…”

Section: Parametrizations At Equilibrium and Potential Of Mean Forcementioning

confidence: 99%

“…In IBI methods, [2], an iterative numerical minimization problem is introduced based onḡ(R). The (pair) CG potential is refined at the iteration (i + 1) according to the following scheme:…”

Section: Parametrizations At Equilibrium and Potential Of Mean Forcementioning

confidence: 99%

“…Methods such as inverse Monte Carlo [1], inverse Boltzmann [2], force matching [3], relative entropy [4], provide parameterizations of coarse-grained effective potentials at equilibrium by minimizing a fitting functional over a parameter space. Then, we further extend these studies using path-space methods (relative entropy rate) for coarse-graining and uncertainty quantification for non-equilibrium processes, [5,6,7,8].…”

Section: Introductionmentioning

confidence: 99%

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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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Deriving effective mesoscale potentials from atomistic simulations

Cited by 1,182 publications

References 34 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

Modeling of Polystyrene under Confinement: Exploring the Limits of Iterative Boltzmann Inversion

From Atomistic to Systematic Coarse-Grained Models for Molecular Systems

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