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
Importance of force decomposition for local stress calculations in biomembrane molecular simulations
TL;DR: This work presents a new implementation of local stress calculations that systematically treats constraints and considers a privileged decomposition, the central force decompositions, that leads to a symmetric stress tensor by construction on biomembranes.
Journal ArticleDOI
A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
Adam Liwo,Maciej Baranowski,Cezary Czaplewski,Ewa I. Gołaś,Ewa I. Gołaś,Yi He,Dawid Jagieła,Paweł Krupa,Paweł Krupa,Maciej Maciejczyk,Mariusz Makowski,Magdalena A. Mozolewska,Magdalena A. Mozolewska,Andrei Niadzvedtski,Stanisław Ołdziej,Harold A. Scheraga,Adam K. Sieradzan,Rafał Ślusarz,Tomasz K Wirecki,Tomasz K Wirecki,Yanping Yin,Bartłomiej Zaborowski,Bartłomiej Zaborowski +22 more
TL;DR: A unified coarse-grained model of three major classes of biological molecules—proteins, nucleic acids, and polysaccharides—has been developed, based on the observations that the repeated units of biopolymers are highly polar and their charge distributions can be represented crudely as point multipoles.
Journal ArticleDOI
Membrane Active Peptides and Their Biophysical Characterization
TL;DR: Recent advances in experimental and computational investigation of membrane active peptides are summarized with particular emphasis on two amphipathic membraneactive peptides, the AMP melittin and the CPP pVEC.
Journal ArticleDOI
Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
TL;DR: The ELNEDIN protein model is replaced with Lennard-Jones interactions based on the contact map of the native protein structure as is done in Go̅-like models, and it can capture the structural motion linked to particular catalytic activity in the Man5B protein, in agreement with all-atom simulations.
Journal ArticleDOI
Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane.
TL;DR: The need for careful parametrization of coarse-grained force fields is illustrated and the utility of atomistic molecular dynamics for providing quantitative thermodynamic and mechanistic analysis of protein-lipid interactions is demonstrated.
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.