arXiv:2506.19628physics.chem-phcs.LG2025-06被引 5

用流模型核改进粗粒化力场,仅凭构象数据就能生成高质量力场。

Operator Forces For Coarse-Grained Molecular Dynamics

  • 基于流模型设计新核函数,替代传统噪声核以减少局部失真。
  • 仅用构象样本即可生成高精度粗粒化力场,无需原子受力数据。
  • 适合缺乏原子力标签的旧数据集,尤其适用于小蛋白系统。

粗粒化(CG)分子动力学通过将相关原子组替换为粗粒化粒子,扩展了原子模拟的长度和时间尺度。机器学习粗粒化(MLCG)已成为构建高精度粗粒化力场的有前景方法。然而,传统力匹配需大量带有对应力标签的原子轨迹,而实际中原子力常未记录,使力匹配在已有数据集上难以应用。近期提出的基于噪声的核函数可适应低数据场景,包括无原子力的情况,但会引入显著的局部畸变。本文提出基于归一化流的更通用核函数,显著降低局部畸变,同时保持全局构象准确性。我们在小蛋白系统上验证了该方法,结果表明流基核函数仅需构象样本即可生成高质量的粗粒化力场。

原文摘要 · Abstract (English)

Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising approach to construct highly accurate force fields for CG molecular dynamics. However, the calibration of MLCG force fields typically hinges on force matching, which demands extensive reference atomistic trajectories with corresponding force labels. In practice, atomistic forces are often not recorded, making traditional force matching infeasible on pre-existing datasets. Recently, noise-based kernels have been introduced to adapt force matching to the low-data regime, including situations in which reference atomistic forces are not present. While this approach produces force fields which recapitulate slow collective motion, it introduces significant local distortions due to the corrupting effects of the noise-based kernel. In this work, we introduce more general kernels based on normalizing flows that substantially reduce these local distortions while preserving global conformational accuracy. We demonstrate our method on small proteins, showing that flow-based kernels can generate high-quality CG forces solely from configurational samples.

粗粒化流模型力场构建机器学习

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