用集体变量加速扩散采样,高效发现分子构象与反应路径。
Enhancing Diffusion-Based Sampling with Molecular Collective Variables
- 引入低维集体变量作为采样引导,通过排斥势推动探索新构象区。
- 在肽类采样中实现多样构象恢复和精确自由能曲线,支持反应过程模拟。
- 首次实现基于扩散模型的反应性采样,速度远超传统方法。
基于扩散的采样器仅依赖能量或对数密度进行高维分布采样,无需训练数据,但在分子系统中效率低下且难以捕捉热力学重要构象。受增强采样启发,本文提出在原子坐标低维投影(即集体变量)上施加序列化偏置,通过近期样本的集体变量构建排斥势,促使后续采样远离已探索区域,等效提升投影空间温度。该方法显著提升采样效率,增强模式发现能力,可估计自由能差,并通过偏差重加权保持对近似玻尔兹曼分布的独立采样。在标准肽类构象采样基准测试中,成功恢复多样构象状态并获得准确自由能轮廓。首次实现基于扩散模型的反应性采样,使用通用原子间势能函数以接近第一性原理精度捕捉键断裂与形成过程。该方法在极短时间内完成反应势能面解析,大幅缩短计算耗时,推动扩散采样向分子科学实用化迈进。
原文摘要 · Abstract (English)
Diffusion-based samplers learn to sample complex, high-dimensional distributions using energies or log densities alone, without training data. Yet, they remain impractical for molecular sampling because they are often slower than molecular dynamics and miss thermodynamically relevant modes. Inspired by enhanced sampling, we encourage exploration by introducing a sequential bias along bespoke, information-rich, low-dimensional projections of atomic coordinates known as collective variables (CVs). We introduce a repulsive potential centered on the CVs from recent samples, which pushes future samples towards novel CV regions and effectively increases the temperature in the projected space. Our resulting method improves efficiency, mode discovery, enables the estimation of free energy differences, and retains independent sampling from the approximate Boltzmann distribution via reweighting by the bias. On standard peptide conformational sampling benchmarks, the method recovers diverse conformational states and accurate free energy profiles. We are the first to demonstrate reactive sampling using a diffusion-based sampler, capturing bond breaking and formation with universal interatomic potentials at near-first-principles accuracy. The approach resolves reactive energy landscapes at a fraction of the wall-clock time of standard sampling methods, advancing diffusion-based sampling towards practical use in molecular sciences.
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