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 ArticleDOI
Systematic coarse graining from structure using internal states : application to phospholipid/cholesterol bilayer
TL;DR: The new model agrees with the original models on large-scale structural features such as density fluctuations in pure dipalmitoylphosphocholine and cholesterol domain formation at intermediate concentrations and also indicates that ordered and disordered domains form at all cholesterol concentrations, even if the global density remains uniform.
Journal ArticleDOI
Stability and dynamics of membrane-spanning DNA nanopores
Vishal Maingi,Jonathan R. Burns,Jaakko J. Uusitalo,Stefan Howorka,Siewert J. Marrink,Mark S.P. Sansom +5 more
TL;DR: Multiscale molecular dynamics simulations are used to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer and inform the design of next-generation DNA pores for synthetic biology or biomedicine.
Journal ArticleDOI
Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model
TL;DR: A structure-based coarse graining methodology which preserves the solvation structure around the peptides in combination with a method to devise nonbonded potentials between peptide beads in a way that the peptide-peptide interaction in water is represented correctly and that results in the correct thermodynamic association behavior.
Journal ArticleDOI
Optimal number of coarse-grained sites in different components of large biomolecular complexes.
TL;DR: The method proposed in this paper is valuable for the optimal construction of CG models of such complexes, and validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems.
Journal ArticleDOI
Adsorption of Plasma Proteins onto PEGylated Lipid Bilayers: The Effect of PEG Size and Grafting Density
Hwankyu Lee,Ronald G. Larson +1 more
TL;DR: The binding between HSAs and bilayers is suppressed by the PEG layer in a brush but not in a mushroom, indicating that the attractive force between proteins and bilayer can overcome the steric effect of the P EG layer in the mushroom state or in the transition region from mushroom to brush.
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.