标题: 伞形采样-关于水油界面作为参考组应该如何定义？ [打印本页] 作者Author: YZR 时间: yesterday 11:34 标题: 伞形采样-关于水油界面作为参考组应该如何定义？ “The thermodynamic preference for the distribution of ligand L and its complexes with Am3+, including AmL(NO3)3, [AmL2(NO3)]2+, [Am(NO3)5]2–, and [AmL(H2O)4]3+, in aqueous (ΔGIW, where the subscript I represents the interface and W represents the aqueous phase) and organic phases (ΔGIO, where the subscript O represents the organic phase) with respect to the interface was evaluated by calculating the potentials of mean force (PMF) using the umbrella sampling technique. [url=](48)[/url] The compositions of the model systems are tabulated in Table1. Starting from the initial conformation with one solute at the interface in the biphasic systems, after a 50 ps equilibration run with an NPT ensemble, the solute was pulled toward the bulk oil phase or the bulk water phase (along z axis) with a force constant of 1000 kJ mol–1 nm–2, and within a distance range of ∼3 nm in each direction, the whole path was divided into a series of windows with a window spacing of 0.1 nm. The position of the solute was characterized by the z-axis distance of its center of mass (COM) from “the interface” (defined by the intersection of the water and oil density curves) [url=](20)[/url] where z = 0. These windows were equilibrated for 500 ps and then used as starting configurations in umbrella sampling simulations with each window sampled for 10 ns. The trajectories of all windows were then analyzed using the weighted histogram analysis method (WHAM) [url=](49,50)[/url] as implemented in the GROMACS (analysis routine g_wham).” J.Phys.Chem.B2020,124,1751−1766我想按照这篇文献用伞形采样计算PMF得到自由能，想请教一下文献中说的参考组是“界面”应该如何在pull中设置参数？还有z=0如何实现？