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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Counterion-mediated cluster formation by polyphosphoinositides
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Deciphering solution scattering data with experimentally guided molecular dynamics simulations.
Alexander Björling,Stephan Niebling,Moreno Marcellini,David van der Spoel,Sebastian Westenhoff +4 more
TL;DR: This work presents a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields, and the molecule of interest is refined toward experimental data using molecular dynamics simulation.
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Hydrocarbons are essential for optimal cell size, division and growth of cyanobacteria
David J. Lea-Smith,Maite L. Ortiz-Suarez,Tchern Lenn,Dennis J. Nürnberg,Laura L. Baers,Matthew P. Davey,Lucia Parolini,Roland G. Huber,Charles A. R. Cotton,Giulia Mastroianni,Paolo Bombelli,Petra Ungerer,Tim J. Stevens,Alison G. Smith,Peter J. Bond,Conrad W. Mullineaux,Christopher J. Howe +16 more
TL;DR: It is proposed that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins.
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Molecular Dynamics Simulations of Ion-Containing Polymers Using Generic Coarse-Grained Models
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Analytical model and multiscale simulations of Aβ peptide aggregation in lipid membranes: towards a unifying description of conformational transitions, oligomerization and membrane damage
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