State point dependence of systematically coarse–grained potentials

Ghosh, Jayeeta; Faller, Roland

doi:10.1080/08927020701275050

Cited by 60 publications

(49 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4,10,13 However, an important drawback of the method is the strong state-point dependence and limited transferability of the potentials. 4,13−16 Nevertheless, studies showed that the temperature transferability can be improved through a careful choice of mapping point(s) 17 and/or inclusion of sufficient chemical detail.…”

Section: Introductionmentioning

confidence: 99%

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

Bayramoglu

Faller

2013

Macromolecules

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Bayramoglu

Faller

2013

Macromolecules

Self Cite

View full text Add to dashboard Cite

show abstract

“…This degeneracy (in a mathematical sense) is perhaps already foreshadowed by the variety of CG methods that have been successfully developed: empirical Leonard Jones (LJ) potentials, 11,18,47 iterative Boltzmann inverseion (IBI), 10,16,17 FM, 5,6 etc.. But even within the context of a single method, statistical under-sampling, numerical error, and uncertainty in target data suggest that it is difficult, if not impossible to identify a unique, optimal force for a given coarse-graining procedure.…”

Section: Discussionmentioning

confidence: 99%

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

Patrone

Rosch

Phelan

2016

The Journal of Chemical Physics

View full text Add to dashboard Cite

Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics (MD). In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as Force-Matching (FM). Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our work flow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.

show abstract

“…Recent research has also demonstrated that the potentials calculated to ensure structural consistency between a particular atomically detailed model and a CG model of the same system can demonstrate significant and nontrivial dependence upon the particular thermodynamic state point used to parametrize the potentials. 44,45,[50][51][52][53][54][55][56] This research indicates that achieving complete transferability 43 of CG model parameters across different conditions is intrinsically in conflict with the CG modeling approach because constructing a reduced representation of an atomically detailed system inevitably involves including some amounts of information regarding its thermodynamic state into the CG representation. Partial transferability of a given set of model parameters can possibly be achieved, but at the cost of sacrificing quantitative consistency.…”

Section: Molecular Dynamics ͑Md͒mentioning

confidence: 99%

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

Krishna

Noid

Voth

2009

The Journal of Chemical Physics

115

View full text Add to dashboard Cite

show abstract

State point dependence of systematically coarse–grained potentials

Cited by 60 publications

References 31 publications

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

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

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

Contact Info

Product

Resources

About