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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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Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation
TL;DR: By combining structural information from cryo-electron microscopy and electron crystallography, this work has constructed an all-atom model of a complete MT and used MD to determine its mechanical properties, which extends the range of systems amenable to the MD method and should enable exciting advances in microscopic knowledge of biology.
Journal ArticleDOI
Structure of native lens connexin 46/50 intercellular channels by cryo-EM
Janette B. Myers,Bassam G. Haddad,Susan O'Neill,Dror S. Chorev,Craig C. Yoshioka,Carol V. Robinson,Daniel M. Zuckerman,Steve L. Reichow +7 more
TL;DR: ‘Hot spots’ of genetic mutations linked to hereditary cataract formation map to the core structural–functional elements identified in Cx46/50, suggesting explanations for many of the disease-causing effects.
Journal ArticleDOI
Transient formation of water-conducting states in membrane transporters
TL;DR: It is proposed that the observed water-conducting states likely represent a universal phenomenon in membrane transporters, which is consistent with their reliance on large-scale motion for function.
Journal ArticleDOI
Identification of Novel Cholesterol-binding Regions in Kir2 Channels
Avia Rosenhouse-Dantsker,Sergei Y. Noskov,Serdar Durdagi,Diomedes E. Logothetis,Irena Levitan +4 more
TL;DR: It is shown that cholesterol may bind to two nonanular hydrophobic regions in the transmembrane domain of Kir2.1 located between adjacent subunits of the channel, suggesting the existence of a novel cholesterol binding motif.
Journal ArticleDOI
Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time
TL;DR: The present study joins other recent efforts to develop advanced sampling techniques in MD to calculate dissociation rates, which are gaining importance in the pharmaceutical field as indicators of drug efficacy.
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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