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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
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Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status
TL;DR: A novel finding is shown in which AgNPs could alter the methylation status of histone, which opens a new avenue to study the biological effects of Ag NPs at sublethal concentrations from the perspective of epigenetic mechanisms.
Journal ArticleDOI
A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties.
TL;DR: There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness, hydrophobic thickness, and lipid volume, and the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures.
Journal ArticleDOI
The density of water in carbon nanotubes
TL;DR: In this paper, the density of water confined in carbon nanotubes of different sizes and chirality is calculated, and three H 2 O filling modes are found and a correlation, which relates the density with the nanotube diameter, is proposed.
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Chloride binding site of neurotransmitter sodium symporters
Adriana Krassimirova Kantcheva,Matthias Quick,Lei Shi,Anne-Marie Lund Winther,Sebastian Stolzenberg,Harel Weinstein,Jonathan A. Javitch,Poul Nissen +7 more
TL;DR: The specific insights from the structures reveal an anion-dependent occlusion mechanism for NSS and shed light on the functional role of chloride binding.
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GPU Virtualization and Scheduling Methods: A Comprehensive Survey
TL;DR: An extensive and in-depth survey of GPU virtualization techniques and their scheduling methods is presented and a perspective on the challenges and opportunities for virtualization of heterogeneous computing environments is delivered.
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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