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
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Proceedings ArticleDOI
Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer
David E. Shaw,J. P. Grossman,Joseph A. Bank,Brannon Batson,J. Adam Butts,Jack C. Chao,Martin M. Deneroff,Ron O. Dror,Amos Even,Christopher H. Fenton,Anthony Forte,Joseph Gagliardo,Gennette Gill,Brian Greskamp,C. Richard Ho,Douglas J. Ierardi,Lev Iserovich,Jeffrey S. Kuskin,Richard H. Larson,Timothy Layman,Li-Siang Lee,Adam Lerer,Chester Li,Daniel Killebrew,Kenneth M. Mackenzie,Shark Yeuk-Hai Mok,Mark A. Moraes,Rolf Mueller,Lawrence J. Nociolo,Jon L. Peticolas,Terry Quan,Daniel Ramot,John K. Salmon,Daniele Paolo Scarpazza,U. Ben Schafer,Naseer Siddique,Christopher W. Snyder,Jochen Spengler,Ping Tak Peter Tang,Michael Theobald,Horia Toma,Brian Towles,Benjamin Vitale,Stanley C. Wang,Cliff Young +44 more
TL;DR: The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of computation with communication, and also allows a wider range of algorithms to run efficiently, enabling many new software-based optimizations.
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Distribution of amino acids in a lipid bilayer from computer simulations.
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Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids.
TL;DR: The FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.
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Computer simulation study of fullerene translocation through lipid membranes.
Jirasak Wong-ekkabut,Svetlana Baoukina,Wannapong Triampo,I-Ming Tang,D. Peter Tieleman,Luca Monticelli,Luca Monticelli +6 more
TL;DR: Computer simulations use computer simulations to explore the translocation of fullerene clusters through a model lipid membrane and the effect of high fulleanne concentrations on membrane properties, suggesting that mechanical damage is an unlikely mechanism for membrane disruption and fullerenes toxicity.
Journal ArticleDOI
Coarse-Graining Methods for Computational Biology
TL;DR: The theoretical underpinnings and history of coarse-grained methods are discussed and the state of the field is summarized, organizing key methodologies based on an emerging paradigm for multiscale theory and modeling of biomolecular systems.
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.