Multiscale modeling of biomolecular systems: in serial and in parallel

Ayton, Gary S.; Noid, W. G.; Voth, Gregory A.

doi:10.1016/j.sbi.2007.03.004

Cited by 396 publications

(386 citation statements)

References 80 publications

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“…Consequently, there has been rapidly growing interest in the development of coarse-grained ͑CG͒ models for investigating such long time-and length-scale processes that cannot be adequately studied with atomically detailed MD simulations. 22,23 Many widely disparate CG models have been described in the literature. The present work considers CG models that consist of classical interacting mass points ͑CG sites͒ that each correspond to one or more atoms in an atomically detailed simulation of the same system.…”

Section: Introductionmentioning

confidence: 99%

“…The MS-CG method thus provides a rigorous "multiscale bridge" between atomistic and CG models. 23 In investigating the statistical mechanical foundations of the MS-CG method, it is convenient to introduce a precise definition of consistent CG models. For the present discussion, a CG model of a system is "consistent" with a particular atomistic model of the same system if ͑1͒ each CG coordinate and momentum has been assigned a well defined meaning as a linear combination of the coordinates and momenta of a subset of the atoms in the atomistic model and if ͑2͒ the equilibrium distribution of coordinates and momenta of the CG model is equal to the distribution determined by the equilibrium distribution function of the atomistic model.…”

Section: Introductionmentioning

confidence: 99%

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The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

Noid

Chu

Ayton

et al. 2008

The Journal of Chemical Physics

728

1,165

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Coarse-grained ͑CG͒ models provide a computationally efficient method for rapidly investigating the long time-and length-scale processes that play a critical role in many important biological and soft matter processes. Recently, Izvekov and Voth introduced a new multiscale coarse-graining ͑MS-CG͒ method ͓J. Phys. Chem. B 109, 2469 ͑2005͒; J. Chem. Phys. 123, 134105 ͑2005͔͒ for determining the effective interactions between CG sites using information from simulations of atomically detailed models. The present work develops a formal statistical mechanical framework for the MS-CG method and demonstrates that the variational principle underlying the method may, in principle, be employed to determine the many-body potential of mean force ͑PMF͒ that governs the equilibrium distribution of positions of the CG sites for the MS-CG models. A CG model that employs such a PMF as a "potential energy function" will generate an equilibrium probability distribution of CG sites that is consistent with the atomically detailed model from which the PMF is derived. Consequently, the MS-CG method provides a formal multiscale bridge rigorously connecting the equilibrium ensembles generated with atomistic and CG models. The variational principle also suggests a class of practical algorithms for calculating approximations to this many-body PMF that are optimal. These algorithms use computer simulation data from the atomically detailed model. Finally, important generalizations of the MS-CG method are introduced for treating systems with rigid intramolecular constraints and for developing CG models whose equilibrium momentum distribution is consistent with that of an atomically detailed model.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

Noid

Chu

Ayton

et al. 2008

The Journal of Chemical Physics

728

1,165

View full text Add to dashboard Cite

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“…To overcome these limitations, coarse grained (CG) models, in which several atoms are grouped together into effective interaction sites (CG beads), are currently being developed by many groups (for an overview, see ref. [3][4][5][6][7][8]. The sampling efficiency is increased up to several orders of magnitude with these CG models.…”

Section: Introductionmentioning

confidence: 99%

“…Further background on the emerging field of multiscale modeling methods can be found in recent reviews. 5,28 In this contribution we present a simple hybrid model, which belongs to the fourth class of multiscale methods implying we consider a system in which a predefined part is represented in full detail, and the remainder at the CG level. The coupling is provided by the atomistic molecules which carry additional, virtual interaction sites, through which they interact with the CG surroundings using standard CG potentials.…”

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

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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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“…However, the higher resolution of the fine-grained representation is often not needed for the entire system, or not necessary for the entire duration of the simulation. For these cases, multiscaling methods are being developed in which different parts of the system are represented in different detail or the level of detail can be smoothly switched from coarse-grained to all-atom and vice versa [2].…”

Section: Introductionmentioning

confidence: 99%

Effects of bundling on the properties of the SPC water model

et al. 2009

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Simultaneous representation of molecules at an all-atom and coarse-grained level, as required by multiscaling molecular dynamics simulations, poses problems for the treatment of small molecules. If more than one of these molecules are mapped to a single coarse-grained interaction site, unrestricted movement in the all-atom representation can make a meaningful correspondence of the coordinates between the two representations impossible. Restricting the relative movement of molecules mapped to the same coarse-grained interaction site solves that problem, but will have consequences for the properties of the model. Here we investigate the effects of introducing bundling to the common simple point charge (SPC) water model and present a bundled water model that preserves important properties of SPC water relevant for multiscaling.

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Multiscale modeling of biomolecular systems: in serial and in parallel

Cited by 396 publications

References 80 publications

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

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

Effects of bundling on the properties of the SPC water model

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