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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
Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain.
TL;DR: It is believed that the complex lipid bilayer more accurately describes a bacterial membrane and suggests the use of it in molecular dynamic simulations rather than simple POPE/POPG membranes.
Journal ArticleDOI
Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel
TL;DR: An almost barrier-less three-ion conduction mechanism involving competing knock-on and “pass-by” processes, intimately linked to signature glutamate ring protonation and structural isomerizations is described.
Journal ArticleDOI
Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations.
TL;DR: The conformational plasticity of Cas9 is revealed and key determinants that allow its large-scale conformational changes during nucleic acid binding and processing are identified and called for novel structure engineering efforts that are of fundamental importance for the rational design of new genome-engineering applications.
Journal ArticleDOI
Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations
Federica Moraca,Jussara Amato,Francesco Ortuso,Anna Artese,Bruno Pagano,Ettore Novellino,Stefano Alcaro,Michele Parrinello,Michele Parrinello,Vittorio Limongelli,Vittorio Limongelli +10 more
TL;DR: FM simulations have elucidated the binding mechanism of the anticancer alkaloid berberine to the human telomeric G4 and computed a quantitatively well-characterized free-energy landscape that allows identifying two low-energy ligand binding modes and the presence of higher energy prebinding states.
Journal ArticleDOI
Investigating the Impact of Polymer Functional Groups on the Stability and Activity of Lysozyme–Polymer Conjugates
Melissa E. Lucius,Rebecca Falatach,Cameron McGlone,Katherine Makaroff,Alex P. Danielson,Cameron Williams,Jay C. Nix,Dominik Konkolewicz,Richard C. Page,Jason A. Berberich +9 more
TL;DR: It is shown by X-ray crystallography that enzyme structure is minimally impacted by modification with the RAFT end group, demonstrating that tailoring polymer functionality can improve conjugate activity and minimize enzymatic inactivation by denaturants.
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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