Iterative unbiasing of quasi-equilibrium sampling

This repository contains the PLUMED-2 input files required to generate the data used in the ITRE publications. ITRE is a method to reweight Molecular Dynamics trajectory biased with a history-dependent potential (such as Metadynamics), and calculate unbiased thermodynamic observables. Since it uses the trajectory itself as a proxy of a grid, its scaling does not depend on the dimensionality of the space explored. In addition, thanks to its formulation, it is less affected by out-of-equilibrium points that characterize the early stages of a biased calculation and are usually discarded. Thanks to this feature, it can be used to increase the statistics when evaluating a thermodynamic observable from biased calculation.

本代码存储库包含了用于生成ITRE系列论文中所用数据的PLUMED-2输入文件。ITRE是一种可对带有历史依赖型势场（如元动力学（Metadynamics））偏置的分子动力学（Molecular Dynamics）轨迹进行重加权，并计算无偏热力学可观测量的方法。由于该方法以轨迹本身作为网格的代理表征，其计算缩放性能不依赖于所探索空间的维度。此外，得益于其算法框架，该方法受偏置模拟计算初期典型的非平衡点的影响更小，而这类点通常会被直接舍弃。凭借这一特性，ITRE可用于提升从偏置模拟计算中评估热力学可观测量时的统计可靠性。