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
More filters
Journal Article
Multiscale Modeling of Four-Component Lipid Mixtures: Domain Composition, Size, Alignment, and Properties of the Phase Interface
TL;DR: Characteristics of bilayer thermodynamic behavior in four-component mixtures are revealed, and a baseline for investigation of the effects of proteins and other lipids on membrane phase properties is provided.
Journal ArticleDOI
Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations
Monica Bulacu,Nicolae Goga,Wei Zhao,Giulia Rossi,Luca Monticelli,Luca Monticelli,Xavier Periole,D. Peter Tieleman,Siewert J. Marrink +8 more
TL;DR: Two approaches to improve the stability and accuracy of coarse-grained molecular dynamics simulations are proposed: dummy-assisted dihedral (DAD), the torsion potential is applied differently: instead of acting directly on the beads, it acts on virtual beads, bound to the real ones.
Journal ArticleDOI
Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics.
Benjamin G. Levine,David N. LeBard,Russell DeVane,Wataru Shinoda,Axel Kohlmeyer,Michael L. Klein +5 more
TL;DR: This work to bridge the gap between laboratory and computational time scales by implementing the coarse-grained (CG) force field into the HOOMD-Blue graphical processing unit (GPU)-accelerated molecular dynamics (MD) software package, which marks a significant step toward the computational prediction of the thermodynamic properties of slowly evolving surfactant systems.
Journal ArticleDOI
Influence of nanoparticle size, loading, and shape on the mechanical properties of polymer nanocomposites.
TL;DR: In this paper, the influence of spherical, triangular, and rod-like nanoparticles on the mechanical properties of a polymer nanocomposite (PNC) via coarse-grained molecular dynamics simulations was studied.
Journal ArticleDOI
A coarse-grained molecular dynamics simulation of a sodium dodecyl sulfate micelle in aqueous solution
Seifollah Jalili,Mojdeh Akhavan +1 more
TL;DR: In this paper, a coarse-grained model was used to simulate a dodecyl sulfate micelle in water using four interaction beads, one for hydrophilic head group and three for the dodecyclic chain.
References
More filters
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.