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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
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Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
TL;DR: Metadynamics is a powerful algorithm that can be used both for reconstructing the free energy and for accelerating rare events in systems described by complex Hamiltonians, at the classical or at the quantum level as discussed by the authors.
Journal ArticleDOI
Force-induced activation of covalent bonds in mechanoresponsive polymeric materials
Douglas A. Davis,Andrew Hamilton,Jinglei Yang,Jinglei Yang,Lee D. Cremar,Dara Van. Gough,Stephanie L. Potisek,Mitchell T. Ong,Paul V. Braun,Todd J. Martínez,Todd J. Martínez,Scott R. White,Jeffrey S. Moore,Nancy R. Sottos +13 more
TL;DR: It is found that pronounced changes in colour and fluorescence emerge with the accumulation of plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the ring-opening reaction is an activated process.
Journal ArticleDOI
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C. Phillips,David J. Hardy,Julio D.C. Maia,John E. Stone,João V. Ribeiro,Rafael C. Bernardi,Ronak Buch,Giacomo Fiorin,Jérôme Hénin,Wei Jiang,Ryan McGreevy,Marcelo C. R. Melo,Brian K. Radak,Robert D. Skeel,Abhishek Singharoy,Yi Wang,Benoît Roux,Aleksei Aksimentiev,Zaida Luthey-Schulten,Laxmikant V. Kale,Klaus Schulten,Christophe Chipot,Emad Tajkhorshid +22 more
TL;DR: The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
Journal ArticleDOI
Current Status of the AMOEBA Polarizable Force Field
Jay W. Ponder,Chuanjie Wu,Pengyu Ren,Vijay S. Pande,John D. Chodera,Michael J. Schnieders,Imran S. Haque,David L. Mobley,Daniel S. Lambrecht,Robert A. DiStasio,Martin Head-Gordon,Gary N. I. Clark,Margaret E. Johnson,Teresa Head-Gordon +13 more
TL;DR: It is shown that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions.
Journal ArticleDOI
Biomolecular Simulation: A Computational Microscope for Molecular Biology
TL;DR: The rapidly evolving state of the art for atomic-level biomolecular simulation is described, the types of biological discoveries that can now be made through simulation are illustrated, and challenges motivating continued innovation in this field are discussed.
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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