sobereva 发表于 2023-7-17 11:16

谢谢老师，我学学！

rpestana94 发表于 2023-7-17 05:39
you should edit the original post to add this comment in it as the rule of the forum says

Abou ...

Thanks for the explanation, I'll think and study what you've just said.

jia1012428 发表于 2023-7-16 10:17
补充下，自由能我用mm/pbsa可以算，但我一般选的都是ns的范围，我可以指定某个时间点吗，比如50ns

you should edit the original post to add this comment in it as the rule of the forum says

About your question, using MDanalysis (a python library) you can easily make a script to get the distance between two atoms during the simualtion.

About the mmpbsa I think you can do it, no pretty sure but what is the point to get it at one frame, if you have a big change in the protein during simualtion try to choose a range where this change is present if you want to see how this affect the MMPBSA result

补充下，自由能我用mm/pbsa可以算，但我一般选的都是ns的范围，我可以指定某个时间点吗，比如50ns