计算化学公社

标题: 请问两个基团之间距离的变化图怎么做 [打印本页]

作者
Author: jia1012428 时间: 2023-7-16 23:16
标题: 请问两个基团之间距离的变化图怎么做
请问老师，我会跑md，请问怎么做出来图中下半部分，即两个基团之间距离的变化。还有，我也不会做特定时间两个基团距离的结构图，就上图中的上半部分，请老师指教，谢谢！

作者
Author: jia1012428 时间: 2023-7-16 23:17
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

作者
Author: rpestana94 时间: 2023-7-17 05:39

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

作者
Author: sobereva 时间: 2023-7-17 11:16
(, 下载次数 Times of downloads: 15)

(, 下载次数 Times of downloads: 14)

作者
Author: jia1012428 时间: 2023-7-17 11:38

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.

作者
Author: jia1012428 时间: 2023-7-17 11:39

sobereva 发表于 2023-7-17 11:16

谢谢老师，我学学！

欢迎光临计算化学公社 (http://bbs.keinsci.com/)