aMD-Reweighting

通常,在aMD完成之后还需要对得到的反应坐标的分布进行reweighting,从而得到无偏的自由能估计。
McCammon group提供了Python脚本”PyReweighting”用于对aMD进行reweithting,其使用方法如下:

PyReweighting 包含常用的reweighting方法,包括:
(1) exponential average that reweights trajectory frames by the Boltzmann factor of the boost potential and then calculates the ensemble average for each bin
(2) Maclaurin series expansion that approximates the exponential Boltzmann factor
(3) cumulant expansion that expresses the reweighting factor as summation of boost potential cumulants.

未完待续..