Molecular dynamics enhanced sampling

Orlowski> S.> Nowak, W. (2007). Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin./owrwa/ of Molecular Modeling, 13, 715. 

Fiber R and M Karplus 1990. Enhanced Sampling in Molecular Dynamics Use of the Time-Dependent Hartree Approximation for a Simulation of Carbon Monoxide Diffusion through Myoglobin. Journal of the American Chemical Society 112 9161-9175. 

An overreaching theme of the present chapter, besides broken ergodicity, has to do with the fact that most of the enhanced sampling methods that we shall discuss address situations in which one cannot clearly identify a reaction coordinate that can be conveniently used to describe the kinetic evolution of the system of interest. While methods for enhanced sampling are designed to yield accurate results faster than regular molecular dynamics or Monte Carlo (MC) methods, it is our belief that there is no perfect method, but that, rather, there are methods that perform better for particular applications. Moreover, it should be noted that, while in instances when a proper reaction coordinate can be identified methods described in other chapters are probably more efficient, they could still benefit by sampling in conformational directions perpendicular to the reaction coordinate. 

In such cases, the MEHMC method could be employed in combination with an enhanced sampling method that deforms the effective energy surface (but preserves the location of the potential minima), such as that in [29, 97]. Likewise, it may be worthwhile to explore the use of a reversible multiple-time-scale molecular dynamics propagator [103] with MEHMC to accelerate the dynamical propagation. 

Nakajima, N. Nakamura, H. Kidera, A., Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides, J. Phys. Chem. B 1997,101, 817-824... 

Elber, R. Karplus, M., Enhanced sampling in molecular-dynamics - use of the time-dependent Hartree approximation for a simulation of carbon-monoxide diffusion through myoglobin, J. Am. Chem. Soc. 1990,112, 9161-9175... 

Hamelberg D, Mongan J, McCammon JA (2004) Enhanced sampling of conformational transitions in proteins using full atomistic accelerated molecular dynamics simulations. Protein Sci 13 76-76... 

Recent single-molecule experimental studies of proteins provide more detailed views of protein motions, and confirm that a wide variety of timescales is involved in, e.g., catalytic action of enzymes [7,14,15,19,33], Of course, molecular dynamics simulations have been used to probe motions in single proteins for many years, and advances in both theory and computational science have made simulations a powerful approach to building theoretical understanding of protein dynamics [1], The recent introduction of accelerated molecular dynamics methods is helpful in this context [11]. Although detailed dynamical information is sacrificed to the enhanced sampling of conformational space in these methods, which have been shown to access conformational fluctuations that are revealed by nuclear magnetic resonance experiments on the millisecond... 

Molecular dynamics and minimization of proteins locally enhanced sampling and free energy calculations along reaction paths by perturbation or thermodynamic integration. Stardent, Silicon Graphics, IBM, and HP workstations, moil-view for visualization of shaded spheres and sticks on Silicon Graphics. Available by anonymous ftp from 128.248.186.70. 

Ways and Means to Enhance the Configurational Sampling of Small Peptides in Aqueous Solution in Molecular Dynamics Simulations... 

P. Minary, G. J. Martyna, and M. E. Tuckerman (2004) Long time molecular dynamics for enhanced conformational sampling in biomolecular systems. Phys. Rev. Lett. 93, p. 150201... 

Okamoto, Y. Generalized-ensemble algorithms Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graph. Model. 2004, 22, 425-39. 

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