如何计算Rg、RMSD曲线图中的各自平均值？

12313

各位老师好，这是某篇文献中对于生物大分子体系分子动力学模拟计算部分，使用gromacs计算。图中标红部分是它提到的平均回旋半径值，想问一下各位老师这个平均回旋半径值，包括后面我还看到了平均RMSD值，这个average是怎么计算的？

student0618

If you have the value of each frame e.g. calculated by gmx analysis tools in a file, you can use many statistical tools to get the average. From awk script to python or even excel.

12313

student0618 发表于 2024-6-22 01:50
If you have the value of each frame e.g. calculated by gmx analysis tools in a file, you can use man ...

sorry,but how to obtain the value of each frame?

student0618

If you use gromacs to do analysis, gmx rms to calculate rmsd, gmx gyrate to calculate radius of gyration. See the tutorial or help message on how to use the tool. The output file e.g. rmsd.xvg is actually a dataset with the rmsd/radius of gyration of each frame that allows you to plot the graph.

For example, here we have the contents of an rmsd.xvg I generated from Dr Justin Lemkul's gromacs tutorial 1:


On top it has some information from gromacs (lines start with '#'), then plotting commands for xmgrace/qtgrace about graph labels and title etc (lines start with '@'). The list of numbers below is the xy dataset with the following format:
time rmsd

That you can use the rmsd values to calculate average with whatever tool you want to use.

dayu8278

如果我没理解错，你把数据放在excel里不就能得到均值么？

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student0618 发表于 2024-6-22 13:06
If you use gromacs to do analysis, gmx rms to calculate rmsd, gmx gyrate to calculate radius of gyra ...

I get it.Thanks  for your help

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dayu8278 发表于 2024-6-22 16:26
如果我没理解错，你把数据放在excel里不就能得到均值么？

好像真的是这样，谢谢你

dayu8278

12313 发表于 2024-6-22 20:57
好像真的是这样，谢谢你

但是也得取平衡后的均值才具有统计意义？

12313

dayu8278 发表于 2024-6-23 21:47
但是也得取平衡后的均值才具有统计意义？

谢谢大佬的提醒