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
Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway
Nicolás G. Bologna,Raphael Iselin,Luciano A. Abriata,Luciano A. Abriata,Alexis Sarazin,Nathan Pumplin,Nathan Pumplin,Florence Jay,Thomas Grentzinger,Matteo Dal Peraro,Matteo Dal Peraro,Olivier Voinnet +11 more
TL;DR: It is shown that the N termini of all plant AGO1s contain a nuclear-localization and nuclear-export signal (NES) that enables AtAGO1 nucleo-cytosolic shuttling in a Leptomycin-B-inhibited manner, diagnostic of CRM1(EXPO1)/NES-dependent nuclear export.
Journal ArticleDOI
Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation.
TL;DR: Computational modeling is able to provide mechanistic insight that explains the context of experimental results and can also take the lead and inspire new directions for experimental research into LDS development, to provide a roadmap for the rational design of LDS based therapies.
Posted Content
More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018
Carsten Kutzner,Szilárd Páll,Martin Fechner,Ansgar Esztermann,Bert L. de Groot,Helmut Grubmüller +5 more
TL;DR: This work benchmarks the GROMACS performance on a diverse set of compute nodes and relates it to the costs of the nodes, which may include their lifetime costs for energy and cooling, to identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GR OMACS 2018 simulation package.
Journal ArticleDOI
Conformation space of a heterodimeric ABC exporter under turnover conditions
Susanne Hofmann,Dovile Januliene,Ahmad Reza Mehdipour,Christoph Thomas,Erich Stefan,Stefan Brüchert,Benedikt T Kuhn,Eric R. Geertsma,Gerhard Hummer,Gerhard Hummer,Robert Tampé,Arne Moeller +11 more
TL;DR: Eight cryo-electron microscopy structures of the ATP-binding cassette exporter TmrAB under turnover conditions characterize the entire transport cycle in a lipid environment and reveal that phosphate release, not ATP hydrolysis, triggers the return of the exporter to the IF conformation.
Journal ArticleDOI
EMMA: A Software Package for Markov Model Building and Analysis
TL;DR: This work provides the software framework EMMA, a systematic way to decompose the state space of the molecular system into substates and to estimate a transition matrix containing the transition probabilities between these substates, which can be analyzed to reveal the metastable states of the system.
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