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1. Introduction
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  2. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
  3. Molecular dynamics

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Illustrative Examples. Computation of the Free Energy.

C Chipot Generalized Coordinates and Lagrangian Formulation. Derivative of the Free Energy.

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

Potential of Mean Constraint Force. Adaptive Biasing Force. Numerical Results.

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Hydration of Water and Methane. Halide Binding to a Calix4Pyrrole Derivative. Implicit Solvent Electrostatics in Biomolecular Simulation. Panel Discussion Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules.

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  • Macromolecule Design and Analysis.

As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.

Stokesian dynamics SD is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. In the microcanonical ensemble simulation of polyvalines, the total energy was conserved satisfactorily with time steps as large as 20 fs.

Molecular dynamics

A helix folding simulation of a synthetic peptide was carried out to show the efficiency of the algorithm in a conformational search. J Comput Chem —, Volume 19 , Issue The full text of this article hosted at iucr. If you do not receive an email within 10 minutes, your email address may not be registered, and you may need to create a new Wiley Online Library account. If the address matches an existing account you will receive an email with instructions to retrieve your username.

Constraint dynamics algorithm for simulation of semiflexible macromolecules

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6. Monte Carlo Simulation

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