论文标题
从粗粒到原子分辨率的分子轨迹的时间相干反向图
Temporally coherent backmapping of molecular trajectories from coarse-grained to atomistic resolution
论文作者
论文摘要
粗晶提供了一种将分子动力学模拟的可实现时间和长度尺度扩展到原子状态实际上可能的方法。可以使用粗粒的模拟有效地进行感兴趣的分子配置,如果重建相应的全原子配置,则可以从中推断出有意义的理化信息。但是,由于许多可行的原子构型可以与一个粗粒结构相关联,因此将丢失的原子细节重新引入粗粒结构中的原子质细节的过程证明了一项艰巨的任务。现有的背景方法是严格基于框架的,依靠启发式方法来代替原子片段和随后的放松,或者以参数化的模型替代了分别和独立于每种粗粒结构的原子坐标的参数化模型。这些方法忽略了以前的轨迹框架的信息,这些信息对于确保反向映射轨迹的时间连贯性至关重要,同时还提供了可能有助于产生更高的原子重建的信息。在这项工作中,我们提出了一种以学习为基础的数据驱动方法,用于时间连贯的背景图,该方法明确地合并了前面的轨迹结构中的信息。我们的方法将有条件的变性自动编码器训练,以根据目标粗粒构型和先前重建的原子构型的非确定性重建原子细节进行训练。我们在两个示例性生物分子系统上展示了我们的背态方法:丙氨酸二肽和微动蛋白。我们表明,我们的反映轨迹准确地恢复了原子轨迹数据的结构,热力学和动力学特性。
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done efficiently using coarse-grained simulations, from which meaningful physicochemical information can be inferred if the corresponding all-atom configurations are reconstructed. However, this procedure of backmapping to reintroduce the lost atomistic detail into coarse-grain structures has proven a challenging task due to the many feasible atomistic configurations that can be associated with one coarse-grain structure. Existing backmapping methods are strictly frame-based, relying on either heuristics to replace coarse-grain particles with atomic fragments and subsequent relaxation, or parameterized models to propose atomic coordinates separately and independently for each coarse-grain structure. These approaches neglect information from previous trajectory frames that is critical to ensuring temporal coherence of the backmapped trajectory, while also offering information potentially helpful to produce higher-fidelity atomic reconstructions. In this work we present a deep learning-enabled data-driven approach for temporally coherent backmapping that explicitly incorporates information from preceding trajectory structures. Our method trains a conditional variational autoencoder to non-deterministically reconstruct atomistic detail conditioned on both the target coarse-grain configuration and the previously reconstructed atomistic configuration. We demonstrate our backmapping approach on two exemplar biomolecular systems: alanine dipeptide and the miniprotein chignolin. We show that our backmapped trajectories accurately recover the structural, thermodynamic, and kinetic properties of the atomistic trajectory data.