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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
Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions.
TL;DR: This work presents an efficient automatized umbrella sampling strategy for calculating multidimensional potential of mean force and demonstrates that a significant smaller number of umbrella windows needs to be employed to characterize the free energy landscape over the most relevant regions without any loss in accuracy.
Journal ArticleDOI
Phosphate release coupled to rotary motion of F1-ATPase
Kei-ichi Okazaki,Gerhard Hummer +1 more
TL;DR: Atomistic molecular dynamics simulations are used to construct a first atomistic conformation of the intermediate state following the 40° substep of rotary motion, and to study the timing and molecular mechanism of inorganic phosphate (Pi) release coupled to the rotation.
Journal ArticleDOI
Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism
Jacob D. Durrant,Sarah E. Kochanek,Lorenzo Casalino,Pek U Ieong,Abigail C. Dommer,Rommie E. Amaro +5 more
TL;DR: Molecular dynamics simulations of this crowded subcellular environment of the pandemic influenza A H1N1 2009 viral envelope, coupled with Markov state model theory, provide a novel framework for studying realistic molecular systems at the mesoscale and quantify the kinetics of the neuraminidase 150-loop transition between the open and closed states.
Journal ArticleDOI
Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain
David J. Kast,L. Michel Espinoza-Fonseca,L. Michel Espinoza-Fonseca,Christina Yi,David D. Thomas +4 more
TL;DR: Two complementary time-resolved fluorescence resonance energy transfer experiments and molecular dynamics simulations are performed to elucidate structural changes in the phosphorylation domain (PD) of smooth muscle regulatory light chain (RLC) bound to myosin, confirming the coexistence of two structural states.
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CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems.
TL;DR: It is hoped that CHARMM-GUI Micelle Builder can be used for simulation studies of various protein/micelle systems to better understand the protein structure and dynamics in micelles as well as distribution of detergents and their dynamics around proteins.
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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