The MARTINI force field : Coarse grained model for biomolecular simulations
TLDR
An improved and extended version of the coarse grained lipid model is presented, coined the MARTINI force field, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds to reproduce the free energies of these chemical building blocks.Abstract:
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.read more
Citations
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Intrinsic map dynamics exploration for uncharted effective free-energy landscapes
Eliodoro Chiavazzo,Roberto Covino,Ronald R. Coifman,C. William Gear,Anastasia S. Georgiou,Gerhard Hummer,Gerhard Hummer,Ioannis G. Kevrekidis,Ioannis G. Kevrekidis +8 more
TL;DR: In this article, the authors describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs) by extracting coarse-grained, macroscopic information from stochastic or atomistic simulations such as molecular dynamics.
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Cellular entry of graphene nanosheets: the role of thickness, oxidation and surface adsorption
TL;DR: In this article, the interaction of graphene nanosheets with a lipid bilayer was studied, focusing on the effects of graphene thicknesses (single/multi-layered graphene), oxidation and surface absorption by lipid molecules.
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Lipid bilayer curvature and pore formation induced by charged linear polymers and dendrimers: the effect of molecular shape.
Hwankyu Lee,Ronald G. Larson +1 more
TL;DR: In this paper, the authors performed molecular dynamics simulations of multiple copies of poly-l-lysine (PLL) and charged polyamidoamine (PAMAM) dendrimers in DMPC bilayers with explicit water using the coarse-grained model developed by Marrink et al.
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Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining.
TL;DR: The algorithms enhance the efficiency and stability of MS-CG computations, and these algorithms are incorporated into the MSCGFM program, and this program can become tractable and regularized efficiently.
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The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures
TL;DR: The validity of this theory is demonstrated numerically by applying it to construct MS-CG models of the Lennard-Jones liquid and simple point charge water model systems.
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