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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
P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape.
TL;DR: Both of the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the kinase resistance.
Journal ArticleDOI
A dual anchoring strategy for the localization and activation of artificial metalloenzymes based on the biotin-streptavidin technology.
Jeremy M. Zimbron,Tillmann Heinisch,Maurus Schmid,Didier R. Hamels,Elisa S. Nogueira,Tilman Schirmer,Thomas R. Ward +6 more
TL;DR: It is shown that introduction of a suitably positioned histidine residue contributes to firmly anchor, via a dative bond, a biotinylated rhodium piano stool complex within streptavidin.
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A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.
TL;DR: A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups, which offers straightforward generalization to systems containing double-stranding DNA and DNA binding proteins.
Journal ArticleDOI
RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles
Nicholas P. Bailey,Trond S. Ingebrigtsen,Jesper Schmidt Hansen,Arno A. Veldhorst,Lasse Bøhling,Claire A. Lemarchand,Andreas Elmerdahl Olsen,Andreas Kvist Bacher,Lorenzo Costigliola,Ulf R. Pedersen,Heine Larsen,Jeppe C. Dyre,Thomas B. Schrøder +12 more
TL;DR: RUMD is a general purpose, high-performance molecular dynamics simulation package running on graphical processing units (GPU's) that has a performance that is comparable to other GPU-MD codes at large system sizes and substantially better at smaller sizes.
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Bringing Molecular Dynamics Simulation Data Into View
TL;DR: It is predicted that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.
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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