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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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Journal ArticleDOI
Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces.
TL;DR: The AFIR method is one of the automated reaction-path search methods developed by the authors, and has been applied extensively to a variety of chemical reactions, such as organocatalysis, organometallic catalysis, and photoreactions.
Journal ArticleDOI
The role of L1 stalk:tRNA interaction in the ribosome elongation cycle
Leonardo G. Trabuco,Eduard Schreiner,John Eargle,Peter V. Cornish,Taekjip Ha,Zaida Luthey-Schulten,Klaus Schulten +6 more
TL;DR: Results from a simulation of the entire ribosome in which the L1 stalk is moved from a half-closed conformation to its open conformation are found to support the hypothesis that L1 stalking opening is involved in tRNA release from the ribosomes.
Journal ArticleDOI
Dynamics of K+ ion conduction through Kv1.2.
TL;DR: This Letter demonstrates that molecular dynamics simulations can provide movies of the overall conduction of K(+) ions through Kv1.2, and identifies the sequence of multi-ion configurations involved in permeation.
Journal ArticleDOI
The Structure of Mycobacterium tuberculosis CYP125 MOLECULAR BASIS FOR CHOLESTEROL BINDING IN A P450 NEEDED FOR HOST INFECTION
Kirsty J. McLean,Pierre Lafite,Colin Levy,Myles R. Cheesman,Natalia Mast,Irina A. Pikuleva,David Leys,Andrew W. Munro +7 more
TL;DR: Structural and catalytic properties of a potential M. tuberculosis drug target enzyme are revealed, and the likely mode by which the host-derived substrate is bound and hydroxylated is revealed.
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Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
TL;DR: A dynamic view of the full-length kinase activation is led to, whereby transitions of the catalytic domain to intermediate configurations with a partially open A-loop are permitted, even while the SH2-SH3 clamp remains fully engaged.
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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