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
FESetup: Automating Setup for Alchemical Free Energy Simulations
TL;DR: FESetup is a new pipeline tool which can be used flexibly within larger workflows to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD.
Journal ArticleDOI
Identification of the gpr55 agonist binding site using a novel set of high potency gpr55 selective ligands
Evangelia Kotsikorou,Karla E. Madrigal,Dow P. Hurst,Haleli Sharir,Diane L. Lynch,Susanne Heynen-Genel,Loribelle Milan,Thomas D.Y. Chung,Herbert H. Seltzman,Yushi Bai,Marc G. Caron,Larry S. Barak,Mary E. Abood,Patricia H. Reggio +13 more
TL;DR: These studies suggest that GPR55 antagonists possess a head region that occupies a horizontal binding pocket extending into the extracellular loop region, a central ligand portion that fits vertically in the receptor binding pocket and terminates with a pendant aromatic or heterocyclic ring that juts out.
Journal ArticleDOI
Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex
Barak Raveh,Jerome M. Karp,Samuel Sparks,Kaushik Dutta,Michael P. Rout,Andrej Sali,David Cowburn +6 more
TL;DR: This study characterize how transport factors diffuse rapidly through multiple layers of disordered phenylalanine-glycine (FG) repeat domains lining the nuclear pore complex, and shows that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites.
Journal ArticleDOI
Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy
Nicolas Coudray,Salvatore Valvo,Minghui Hu,Ralph Lasala,Changki Kim,Martin Vink,Ming Zhou,Davide Provasi,Marta Filizola,Juoehi Tao,Jia Fang,Pawel A. Penczek,Iban Ubarretxena-Belandia,David L. Stokes +13 more
TL;DR: Cryoelectron microscopy and molecular dynamics simulation of YiiP in a lipid environment were used to address the feasibility of a conformational change that involves pivoting of a transmembrane, four-helix bundle relative to the M3-M6 helix pair.
Journal ArticleDOI
Exploration, Sampling, And Reconstruction of Free Energy Surfaces with Gaussian Process Regression
TL;DR: It is found that biasing with metadynamics, measuring a free energy gradient estimator, and reconstructing using Gaussian process regression can give an order of magnitude reduction in computational cost.
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