# Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations Source: [Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations]() Collection index: [llms.txt]() Data updated: 2025-10-27T03:02:27.288Z Authors: Gerhard Hummer, Ioannis G. Kevrekidis Published: 2002-12-30T19:36:12.000Z ## 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. ## Recorded benchmark results A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage. ## Original sources and implementation [Original paper]() [PDF]()