From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field

Machado, Matías; Zeida, Ari; Darré, Leonardo; Pantano, Sergio

doi:10.1098/rsfs.2018.0085

Cited by 22 publications

(25 citation statements)

References 128 publications

(177 reference statements)

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“…This can be extremely useful since, despite the fact that the "cellmultipole" method is frequently used in a myriad of systems, it is rarely employed in molecular fluids. In summary, RelRes can become a beneficial tool for molecular simulations, and it has already been acknowledged as such by several review articles [56,57]. butterflies in Fig.…”

Section: Discussionmentioning

confidence: 96%

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Relative Resolution: A multipole approximation at appropriate distances

Chaimovich

Kremer

Peter

2019

Phys. Rev. Research

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Recently, we introduced Relative Resolution (RelRes) as a hybrid formalism for fluid mixtures [Chaimovich et al., J. Chem. Phys. 143, 243107 (2015)]. The essence of this approach is that it switches molecular resolution in terms of relative separation: While nearest neighbors are characterized by a detailed fine-grained model, other neighbors are characterized by a simplified coarse-grained model. Once the two models are analytically connected with each other via energy conservation, RelRes can capture the structural and thermal behavior of various multicomponent and multiphase systems across state space. This current work is a natural continuation of our original communication. Most importantly, we present the comprehensive mathematics of RelRes, casting it as a multipole approximation at appropriate distances; the current set of equations technically applies for any arbitrary system in soft matter (e.g., water). Besides, we continue examining the capability of this multiscale approach in molecular simulations of various (nonpolar) uniform liquids, specifically examining a 2:1 mapping for dumbbell-like molecules, as well as a 6:1 mapping and a 6:2 mapping for butterflylike molecules. In turn, we exhaustively show that RelRes can successfully retrieve for these systems their static and dynamic behavior, given that the fine-grained and coarse-grained potentials are switched at the boundary between the first and second coordination shells, the location at which orientational correlations vanish. We finally conclude by discussing how RelRes is the inherent variant of the "cell-multipole" approach for molecular simulations and, thus, this multiscale framework is especially promising for studying biological systems.

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Section: Discussionmentioning

confidence: 96%

“…If the product rule for the FG coefficients applies [i.e., Eqs. (57) and (58)], then the product rule for the CG coefficients applies [i.e., Eqs. (61) and (62)]; in turn, one can use instead Eqs.…”

Section: Discussionmentioning

confidence: 99%

Relative Resolution: A multipole approximation at appropriate distances

Chaimovich

Kremer

Peter

2019

Phys. Rev. Research

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“…Crnjar et al [1] start their discussion of ligand-gated ion channel models with first principle methods based on the density functional theory, a common computational quantum mechanical approach. A similar quantum mechanical starting point is mentioned in Machado et al [2], which use double-stranded DNA as their illustrative example.…”

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confidence: 87%

Multi-resolution simulations of intracellular processes

2019

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“…The different resolutions may be deployed sequentially, or concurrently [28]; in the latter, the resolution of each particle can be fixed, adaptable, or decoupled via virtual sites. These various strategies and their different implementations were recently reviewed by Machado et al [29].…”

Section: Introductionmentioning

confidence: 99%

Computational methods for exploring protein conformations

Allison

2020

Biochemical Society Transactions

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Proteins are dynamic molecules that can transition between a potentially wide range of structures comprising their conformational ensemble. The nature of these conformations and their relative probabilities are described by a high-dimensional free energy landscape. While computer simulation techniques such as molecular dynamics simulations allow characterisation of the metastable conformational states and the transitions between them, and thus free energy landscapes, to be characterised, the barriers between states can be high, precluding efficient sampling without substantial computational resources. Over the past decades, a dizzying array of methods have emerged for enhancing conformational sampling, and for projecting the free energy landscape onto a reduced set of dimensions that allow conformational states to be distinguished, known as collective variables (CVs), along which sampling may be directed. Here, a brief description of what biomolecular simulation entails is followed by a more detailed exposition of the nature of CVs and methods for determining these, and, lastly, an overview of the myriad different approaches for enhancing conformational sampling, most of which rely upon CVs, including new advances in both CV determination and conformational sampling due to machine learning.

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From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field

Cited by 22 publications

References 128 publications

Relative Resolution: A multipole approximation at appropriate distances

Relative Resolution: A multipole approximation at appropriate distances

Multi-resolution simulations of intracellular processes

Computational methods for exploring protein conformations

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