'For simulations of PNiPAM, parameters remain the same as for PEG if not stated otherwise. For PNiPAM we use a recently modified version of the OPLS-AA force field with partial charges optimized by comparison to quantum mechanical simulations together with the SPC/E water model. (42−45) The first and the last C atom of the backbone of H–[C6H11NO]20–H, which are adjacent to the side chain of the polymer, are defined as pulling groups. A constant force between 1 pN and 500 pN is applied in the z direction. We simulate isotactic (meso-diad) PNiPAM, where the side chains are located on one side of the backbone, and syndiotactic (racemo-diad) PNiPAM, where the side chains are on alternating sides of the chain. The elongated chain is placed in a 3 nm × 3 nm × 11 nm box with 3121 SPC/E water molecules. Each pulling simulation is performed for at least 1000 ns. The temperature remains unchanged throughout a single simulation run and is set to 288, 298, 308, and 318 K, respectively.'
（1）请问是如何实现的？（2）GMX是否有办法能像该文章实验部分AFM单分子力谱原理图中演示的那样将分子固定在某一平面上，测量对温度引起的链塌缩对另一端探针施加的力？（3）对于文章类似的体系但分子量较大的情况（文章中PNIPAM聚合度为20，想计算一个约150聚合度的单链）是否有必要做粗粒化模拟以及用什么软件更合适？请大家不吝赐教，谢谢！作者Author: sobereva 时间: 2022-7-1 05:10
用pull设置
只要全原子算得动，就没任何必要用粗粒化作者Author: LBH0532 时间: 2022-7-14 13:27