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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
Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions
Alexey K. Shaytan,G. A. Armeev,Alexander Goncearenco,Victor B. Zhurkin,David Landsman,Anna R. Panchenko +5 more
TL;DR: An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin, suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of hist one tail modifications and binding of the effector proteins.
Journal ArticleDOI
Lipid Gymnastics: Evidence of Complete Acyl Chain Reversal in Oxidized Phospholipids from Molecular Simulations
TL;DR: This work provides the first molecular evidence of the "extended lipid conformation" in phospholipid membranes, as the chain reversal of PazePC lipids decorates the membrane interface with reactive, negatively charged functional groups.
Journal ArticleDOI
CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
TL;DR: Enhanced molecular dynamics simulations are performed in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics methodology, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis, explaining how the HNH domain exerts a conformational control domain over DNA cleavage.
Journal ArticleDOI
Structural Determinants of Cadherin-23 Function in Hearing and Deafness.
TL;DR: The structures define an uncharacterized cadherin family and, with simulations, suggest mechanisms underlying inherited deafness and how cadher in-23 may bind with itself and with protocadherin-15 to form the tip link.
Journal ArticleDOI
Dynamics of water and solute transport in polymeric reverse osmosis membranes via molecular dynamics simulations
TL;DR: In this paper, the authors studied the transport characteristics of water and six different solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, using non-equilibrium molecular dynamics simulations.
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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