Open AccessBook
Scalable Molecular Dynamics with NAMD
About:
The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
Citations
More filters
Journal ArticleDOI
Quantitative Modeling of Membrane Deformations by Multihelical Membrane Proteins: Application to G-Protein Coupled Receptors
TL;DR: A novel multiscale computational approach for quantifying the hydrophobic mismatch-driven remodeling of membrane bilayers by multihelical membrane proteins is presented and how distinct ligand-induced conformations of G-protein coupled receptors may elicit different functional responses through differential effects on the membrane environment is suggested.
Journal ArticleDOI
Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions
TL;DR: Structural plasticity plays a major role in determining differential binding of CXCL8 monomer and dimer to glycosaminoglycans (GAGs) and that dimer is the high-affinity GAG ligand.
Journal ArticleDOI
Structure, dynamics, and activity of xylanase solvated in binary mixtures of ionic liquid and water.
Vance Jaeger,Jim Pfaendtner +1 more
TL;DR: Dynamic light scattering and kinetic studies indicate that likely factors in the loss of enzyme activity for this xylanase are the dampening of dynamic motion and kinetic trapping of cations in the binding pocket as opposed to the denaturing of the protein.
Journal ArticleDOI
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations
TL;DR: The proposed approach provides a feasible mechanism to quickly construct the global free energy profile and identify free energy barriers and basins in free energy simulations via a robust, variational procedure that determines an analytic representation of thefree energy profile without the requirement of numerically unstable histograms or binning procedures.
Journal ArticleDOI
TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries
TL;DR: TTClust (for Trusty Trajectory Clustering), a python program that uses the MDTraj package to fill the need for an easy-to-use clustering program with complete user control, taking as input a trajectory from any molecular dynamics package and outputting an intuitive display of results with plots allowing at-a-glance analysis.
References
More filters
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.
Related Papers (5)
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell,D. Bashford,M. Bellott,Roland L. Dunbrack,Jeffrey D. Evanseck,Martin J. Field,Stefan Fischer,Jiali Gao,H. Guo,S. Ha,Diane Joseph-McCarthy,L. Kuchnir,K. Kuczera,F. T. K. Lau,C. Mattos,Stephen W. Michnick,Thien H. Ngo,D. T. Nguyen,B. Prodhom,W. E. Reiher,Benoît Roux,M. Schlenkrich,Jeremy C. Smith,Roland H. Stote,John E. Straub,Masakatsu Watanabe,J. Wiórkiewicz-Kuczera,D. Yin,Martin Karplus +28 more