论文标题
通过温度加速切片的采样和平行偏置的组合，改善高维自由能景观的探索
Improving the Exploration of High Dimensional Free Energy Landscape by a Combination of Temperature Accelerated Sliced Sampling and Parallel Biasing
论文作者
论文摘要
在自由能计算中，有偏见的采样方法，例如可以探索高维集合变量（CV）空间的温度加速采样（TASS）。即使使用了大量的偏置CV，而许多常规方法仅限于两个或三个CV，这种方法也可以有效地采样配置空间。在本文中，我们提出了对Tass方法的修改，称为平行偏置tass或pBTAS，其中在选定的CVS集合集合中纳入了多维平行元动力学偏置。得出了相应的时间相关的重新加权方程，并根据基准测试了该方法。特别是，我们将PBTAS的准确性和效率与各种方法进行比较。标准的TAS，温度加速分子动力学/驱动 - 无绝热的自由能动力学和平行偏置元动力学。我们通过从25 ns长轨迹中重建真空丙氨酸的八维自由能表面来证明PBTASS方法的能力。据报道，该系统高维自由能景观上的高能鞍点的自由能屏障和自由能。
Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free energy calculations. Such methods can efficiently sample configurational space even when a large number of CVs for biasing are used while many conventional methods are limited to two or three CVs. In this paper, we propose a modification to the TASS method, called Parallel Bias TASS or PBTASS, wherein a multidimensional parallel metadynamics bias is incorporated on a selected set of CVs. The corresponding time-dependent reweighting equations are derived, and the method is benchmarked. In particular, we compare the accuracy and efficiency of PBTASS with various methods viz. standard TASS, Temperature Accelerated Molecular Dynamics/driven-Adiabatic Free Energy Dynamics, and Parallel Bias Metadynamics. We demonstrate the capability of the PBTASS method by reconstructing the eight-dimensional free energy surface of alanine pentapeptide in vacuo from a 25 ns long trajectory. Free energy barriers and free energies of high energy saddle points on the high dimensional free energy landscape of this system are reported.
