求助：Gromacs如何施加恒定力或测试因分子变形产生的拉力？

LBH0532

如题，在J. Am. Chem. Soc. 2019, 141, 29, 11603–11613中，作者提到

'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！

mgqqlwq

楼主想麻烦问下您最后是通过两端都加力的方式呢，还是通过固定一端另外一端加力呢？
固定一端另外一端加力的方式我参考别人的方式可以实现，但是两端都加力的方式我实现不了，Pull的设置我不知道该如何设定

sobereva

LBH0532 发表于 2022-7-14 13:27
谢谢sob大，请问pnipam在LCST温度以上平衡后是球状一团的，想要像文章中一样只拉伸两端基碳原子是否可以 ...

可以固定一头

LBH0532

sobereva 发表于 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

谢谢sob大，请问pnipam在LCST温度以上平衡后是球状一团的，想要像文章中一样只拉伸两端基碳原子是否可以固定其中一端的位置，方便在不同的拉力情况下比较直观的对比链长

sobereva

用pull设置
只要全原子算得动，就没任何必要用粗粒化