A High-Dimensional Lab-Frame Model of Markovian Dynamics in Alanine Dipeptide
Abstract
We present a high-dimensional coarse-grained model of alanine dipeptide that explicitly incorporates global translation and rotation alongside internal conformational dynamics. Using atomistic molecular dynamics trajectories, we construct a 10-bead Markovian Langevin model with a 24-dimensional internal potential of mean force and a full matrix of site-specific friction coefficients. The equilibrium landscape is represented by a Gaussian mixture model, while a rotational-entropy correction accounts for the coupling between internal conformation and global molecular motion. Friction coefficients are obtained using a generalized Einstein relation based on time-correlation functions. We show that the rotational-entropy correction is essential for obtaining a physically admissible friction matrix and significantly affects the inferred dynamics. Without fitting to coarse-grained dynamical observables, the resulting model reproduces a broad range of atomistic auto- and cross-correlation functions. The result is a compact and interpretable dynamical representation of the entire peptide at the chosen CG resolution, which explicitly preserves distinctions between energetic and dissipative coupling over a wide range of motions, including those between conformational fluctuations and global translational and rotational diffusion.
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BibTeX
@misc{hall2026highdimensional,
title = {{A High-Dimensional Lab-Frame Model of Markovian Dynamics in Alanine Dipeptide}},
author = {Jesse M. Hall and Marina G. Guenza},
howpublished = {arXiv},
year = {2026},
month = nov,
doi = {10.48550/arxiv.2611.07200},
eprint = {2611.07200},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2611.07200},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - A High-Dimensional Lab-Frame Model of Markovian Dynamics in Alanine Dipeptide
AU - Jesse M. Hall
AU - Marina G. Guenza
PY - 2026
DA - 2026/11/04
PB - arXiv
DO - 10.48550/arxiv.2611.07200
UR - https://arxiv.org/abs/2611.07200
AB - We present a high-dimensional coarse-grained model of alanine dipeptide that explicitly incorporates global translation and rotation alongside internal conformational dynamics. Using atomistic molecular dynamics trajectories, we construct a 10-bead Markovian Langevin model with a 24-dimensional internal potential of mean force and a full matrix of site-specific friction coefficients. The equilibrium landscape is represented by a Gaussian mixture model, while a rotational-entropy correction accounts for the coupling between internal conformation and global molecular motion. Friction coefficients are obtained using a generalized Einstein relation based on time-correlation functions. We show that the rotational-entropy correction is essential for obtaining a physically admissible friction matrix and significantly affects the inferred dynamics. Without fitting to coarse-grained dynamical observables, the resulting model reproduces a broad range of atomistic auto- and cross-correlation functions. The result is a compact and interpretable dynamical representation of the entire peptide at the chosen CG resolution, which explicitly preserves distinctions between energetic and dissipative coupling over a wide range of motions, including those between conformational fluctuations and global translational and rotational diffusion.
ER -