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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Comparative assessment of the ELBA coarse-grained model for water
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α-Synuclein-Induced Membrane Remodeling Is Driven by Binding Affinity, Partition Depth, and Interleaflet Order Asymmetry
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Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function.
TL;DR: The currently available data is summarized with regard to the formation of GPCR oligomers, their structures and dependency on the membrane microenvironment as well as the coupling of oligomerization to receptor function.
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The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials.
TL;DR: This work shows that the MS-CG method recovers only part of the atomistic free-energy landscape in the coarse-grain coordinates, and introduces density dependent MS- CG potentials, which are examined in simulations of nitromethane under various thermodynamic conditions, including shocked states.
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Determining the bending modulus of a lipid membrane by simulating buckling
TL;DR: This work systematically derive highly accurate analytical expressions for the forces along and perpendicular to the buckle, and elucidate some of their counterintuitive properties using the framework of a surface stress tensor.
References
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Book
CRC Handbook of Chemistry and Physics
TL;DR: CRC handbook of chemistry and physics, CRC Handbook of Chemistry and Physics, CRC handbook as discussed by the authors, CRC Handbook for Chemistry and Physiology, CRC Handbook for Physics,
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Book
Intermolecular and surface forces
TL;DR: The forces between atoms and molecules are discussed in detail in this article, including the van der Waals forces between surfaces, and the forces between particles and surfaces, as well as their interactions with other forces.
Journal ArticleDOI
GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Journal ArticleDOI
GROMACS 3.0: a package for molecular simulation and trajectory analysis
TL;DR: The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2.