Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations

By Gerhard Hummer, Ioannis G. Kevrekidis. 2002

238 citations recorded by the source corpus.

We present a “coarse molecular dynamics” approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables. Techniques from traditional numerical analysis (Newton–Raphson, coarse projective integration) are thus enabled; these techniques help analyze important features of the free-energy landscape (coarse transition states, eigenvalues and eigenvectors, transition rates, etc.). Reverse integration of coarse variables backward in time can assist escape from free energy minima and trace low-dimensional free energy surfaces. To illustrate the coarse molecular dynamics approach, we combine multiple short (0.5 ps) replica simulations to map the free energy surface of the “alanine dipeptide” in water, and to determine the ∼1/(1000 ps) rate of interconversion between the two stable...

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/359b0ea0aeb9717e764a74cda8bf0b1e2ecca0e0

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In Atomic and Molecular Physics, and Optics

In Molecular Biology

Citations in the corpus

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems (2008, methodology): “Specifically, following the equation-free coarse molecular dynamics approach [31, 32, 33], we propose to explore the effective free energy and diffusion coefficients as a function of the diffusion map coordinates by a series of multiple short simulations appropriately initialized at given values of ”
Biological and synthetic membranes: What can be learned from a coarse-grained description? (2006, background): ““Systematic” coarse-graining procedures [12,14–17,210] or tightly coupled multi-scale simulation techniques [210,229,251,436,437] will provide information about the specific interactions that have to be incorporated into coarse-grained models to describe the phenomena of interest.”
Equation-free: The computer-aided analysis of complex multiscale systems (2004, background): “…of catalytic surface reactions (Makeev et al., 2002a,b, 2004; Rico-Martinez et al., 2004), and MD simulations of the folding of a peptide fragment (Hummer and Kevrekidis, 2003) to individual-based models of evolving diseases (Cisternas et al., 2004) and e-coli chemotaxis (Setayeshgar et al.,…”