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Scalable Molecular Dynamics with NAMD
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The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
Citations
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Journal ArticleDOI
Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field.
Chen-Yu Li,Elisa A. Hemmig,Jinglin Kong,Jejoong Yoo,Silvia Hernández-Ainsa,Ulrich F. Keyser,Aleksei Aksimentiev +6 more
TL;DR: A comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics simulations and nanocapillary electric current recordings and demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA.
Journal ArticleDOI
A review of advancements in coarse-grained molecular dynamics simulations
TL;DR: In this article, coarse-grained molecular dynamics has emerged as a way to model large and complex systems in an efficient and inexpensive manner due to its lowered resolution, faster dynam...
Journal ArticleDOI
Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.
TL;DR: Two atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement are developed and simulated, demonstrating the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.
Journal ArticleDOI
Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4).
TL;DR: The binding mode obtained by automatic docking is exploited for the optimization of these EphB4 inhibitors by chemical synthesis and compound 66 shows very high affinity for a few other tyrosine kinases with threonine as gatekeeper residue (Abl, Lck, and Src).
Journal ArticleDOI
Complete Ion-Coordination Structure in the Rotor Ring of Na+-Dependent F-ATP Synthases
Thomas Meier,Alexander Krah,Peter J. Bond,Denys Pogoryelov,Kay Diederichs,José D. Faraldo-Gómez +5 more
TL;DR: Following an updated crystallographic analysis of the c-ring from Ilyobacter tartaricus, the complete ion-coordination structure of the Na(+) sites is reported, revealing an ancient strategy for selective ion coupling in ATP synthases.
References
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Journal ArticleDOI
Generalized Gradient Approximation Made Simple
TL;DR: A simple derivation of a simple GGA is presented, in which all parameters (other than those in LSD) are fundamental constants, and only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked.
Journal ArticleDOI
Self-Consistent Equations Including Exchange and Correlation Effects
Walter Kohn,L. J. Sham +1 more
TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
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.
Journal ArticleDOI
Density-functional exchange-energy approximation with correct asymptotic behavior.
TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
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