dorsal/arxiv
View SchemaCoarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations
| Authors | Gerhard Hummer, Ioannis G. Kevrekidis |
|---|---|
| Categories | |
| ArXiv ID | physics/0212108 |
| URL | https://arxiv.org/abs/physics/0212108 |
| DOI | 10.1063/1.1574777 |
Abstract
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 (irreversible) expected 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 configurational basins corresponding to the alpha-helical and extended minima.
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"abstract": "We present a ``coarse molecular dynamics\u0027\u0027 approach and apply it to studying\nthe kinetics and thermodynamics of a peptide fragment dissolved in water. Short\nbursts of appropriately initialized simulations are used to infer the\ndeterministic and stochastic components of the peptide motion parametrized by\nan appropriate set of coarse variables. Techniques from traditional numerical\nanalysis (Newton-Raphson, coarse projective integration) are thus enabled;\nthese techniques help analyze important features of the free-energy landscape\n(coarse transition states, eigenvalues and eigenvectors, transition rates,\netc.). Reverse integration of (irreversible) expected coarse variables backward\nin time can assist escape from free energy minima and trace low-dimensional\nfree energy surfaces. To illustrate the ``coarse molecular dynamics\u0027\u0027 approach,\nwe combine multiple short (0.5-ps) replica simulations to map the free energy\nsurface of the ``alanine dipeptide\u0027\u0027 in water, and to determine the ~ 1/(1000\nps) rate of interconversion between the two stable configurational basins\ncorresponding to the alpha-helical and extended minima.",
"arxiv_id": "physics/0212108",
"authors": [
"Gerhard Hummer",
"Ioannis G. Kevrekidis"
],
"categories": [
"physics.chem-ph",
"physics.bio-ph",
"physics.comp-ph"
],
"doi": "10.1063/1.1574777",
"title": "Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations",
"url": "https://arxiv.org/abs/physics/0212108"
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