Coarse-graining conformational dynamics with multi-dimensional generalized Langevin equation: how, when, and why
<|reference_start|>Coarse-graining conformational dynamics with multi-dimensional generalized Langevin equation: how, when, and why: A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained conformational dynamics. Constrained by the fluctuation-dissipation theorem, the approach can build coarse-grained models in dynamical consistency with all-atom molecular dynamics. We also propose practical criteria for AIGLE to enforce long-term dynamical consistency. Case studies of a toy polymer, with 20 coarse-grained sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling coarse-grained conformational dynamics in practice.<|reference_end|>
@article{xie2024coarse-graining,
    title={Coarse-graining conformational dynamics with multi-dimensional
  generalized Langevin equation: how, when, and why},
    author={Pinchen Xie, Yunrui Qiu, Weinan E},
    journal={arXiv preprint arXiv:2405.12356},
    year={2024},
    doi={10.1021/acs.jctc.4c00729},
    archivePrefix={arXiv},
    eprint={2405.12356},
    primaryClass={physics.bio-ph cs.LG physics.chem-ph physics.data-an}
}