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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
Structural insights into differences in G protein activation by family A and family B GPCRs.
Daniel Hilger,Kaavya Krishna Kumar,Hongli Hu,Mie Fabricius Pedersen,Evan S. O'Brien,Lise Giehm,Christine Jennings,Gozde Eskici,Asuka Inoue,Michael T. Lerch,Jesper Mosolff Mathiesen,Georgios Skiniotis,Georgios Skiniotis,Brian K. Kobilka +13 more
TL;DR: The missing conserved structural motifs found in family A GPCRs together with the marked differences in the conformation of TM6 in the active state suggest distinct activation mechanisms between family B and family AGPCRs.
Journal ArticleDOI
A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values.
Michael J. Harms,Jamie L. Schlessman,Jamie L. Schlessman,Michael S. Chimenti,G. Sue,Ana Damjanović,E Bertrand García-Moreno +6 more
TL;DR: In molecular dynamics simulations, the ion pair between Lys‐38 and Glu‐122 is unstable and a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys‐ 38, illustrating both the important roles of local flexibility and water penetration as determinants of pKa values of ionizable groups buried near the protein–water interface.
Journal ArticleDOI
Transition States in a Protein Environment - ONIOM QM:MM Modeling of Isopenicillin N Synthesis.
TL;DR: The analysis suggests that the main catalytic effect comes from the metal center, while the protein controls the reactivity to achieve high product specificity.
Journal ArticleDOI
Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes
Binquan Luan,Aleksei Aksimentiev +1 more
TL;DR: It is demonstrated that inversion of the DNA's electrophoretic mobility results from a complex interplay of electrostatics and hydrodynamics.
Proceedings ArticleDOI
ACR: automatic checkpoint/restart for soft and hard error protection
TL;DR: ACR is demonstrated: an automatic checkpoint/restart framework that performs application replication and automatically adapts the checkpoint period using online information about the current failure rate and proposes three recovery schemes that explore the trade-off between performance and reliability requirements.
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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