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标题: 求好用的绘制自由能形貌图的工具 [打印本页]

作者
Author: 12313 时间: 2024-7-5 22:05
标题: 求好用的绘制自由能形貌图的工具
各位老师好，我想知道有没有推荐的绘制自由能形貌图的工具，目前我看网上有用origin绘制的，还有没有什么其他的推荐吗？

作者
Author: student0618 时间: 2024-7-6 00:52
本帖最后由 student0618 于 2024-7-6 04:18 编辑

Do you need the tool to calculate the free energy landscape from a histogram/probability distribution? Do you need the tool to do any kind of reweighting? Or just to do the plot? What is the format of the dataset you have? Is it a 1D, 2D, 3D... dataset? Better be specific in your question!

I assume you're (1) skipping origin and (2) want to use a free alternative here.

If you already have the dataset, not sure if it's 1D, 2D, 3D or ND, and you just need to plot a graph

Python is popular for data analysis. This thread http://bbs.keinsci.com/thread-20056-1-1.html has a python tool to plot a 2D xpm dataset from gmx.
Note: for other plotting tools, you may need to convert file format if your dataset is xpm.
For a quick view of a dataset I usually use gnuplot (1D-3D data, command line/script based, can be used to visualize datasets formated with multiple columns) or QtGrace/xmgrace (1D data, can visualize 2-column dataset and the xvg files output by many programs like gromacs).
To produce a beautiful graph in a GUI I like veusz after trying many alternatives, its customizable and easy to call it from a script once I'm happy with the look. Forgot if it can read xpm, I mainly work on other formats.

If you need to calculate the free energy surface:

Make sure you know how to select the reaction coordinate and the CV you'd like to analyze.
It really depends on you sampling method, is it conventional, unbiased MD? (be careful if its the case, sampling efficiency can be low)
Is it a kind of enhanced sampling method? Many methods e.g. free energy methods in plumed or colvars/ GaMD in Amber or NAMD / metadynamics in several tools / umbrella sampling in e.g. gmx, have their own tool or would suggest a certain method to do rewighting / to remove the bias in the data, then calculate the free energy surface. Once you get the data of your free energy surface, whether its 1D or multidimensional, you can plot it with your favorite plotting tool.
If you know some python (or R), there are many popular packages to process your raw data and do the plots.

作者
Author: 12313 时间: 2024-7-6 17:41
本帖最后由 12313 于 2024-7-6 17:43 编辑

student0618 发表于 2024-7-6 00:52
Do you need the tool to calculate the free energy landscape from a histogram/probability distributio ...

The gibbs.xpm obtained from command gmx sham was converted into text files including xyz coordinated by script with xpm2all.bsh.I don't know whether the format of the dataset is XYZ.I wanna plot 3D graph

作者
Author: student0618 时间: 2024-7-6 18:26
You can open the file in a text editor to check how it looks, or even excel.

There are many free software that let you plot a 3D graph. Both gnuplot (command line) and veusz (GUI) I've mentioned let you do it, and they're just the software I prefer personally. If they are still hard to use you may search for other alternatives, many plotting tools out there with a user-friendly GUI.

作者
Author: 12313 时间: 2024-7-6 19:35

student0618 发表于 2024-7-6 18:26
You can open the file in a text editor to check how it looks, or even excel.

There are many free ...

I have been checked the file in a text editor, and I found many repetitive parts of datasets in the file, is that normal?
Actually,I want to make 3D graph like these pictures,which are extracted from articles.but I don't know what softwares they are made by.
(, 下载次数 Times of downloads: 22) (, 下载次数 Times of downloads: 23)

作者
Author: student0618 时间: 2024-7-7 00:45
本帖最后由 student0618 于 2024-7-7 02:26 编辑

I used the free (and open-source) software veusz to plot your data provided in another thread "使用gmx sham获得gibbs.xpm文件后，使用xpm2all.bsh将gibbs.xpm进行转化 http://bbs.keinsci.com/forum.php ... 47029&fromuid=64740". I didn't use gnuplot or other tools since they're not on this computer.

I loaded your file with the "gnuplot 2D data plugin".
Colored with the "spectrum2" colormap and inverted color scale, there are more colormaps if you don't like it. Didn't put axis label to save time.
(, 下载次数 Times of downloads: 24)
For the 2D plot I used "resample-smooth" option to get a better looking, also added contour line (forgot at what level, just playing around).
A bit tricky to get the color of the 3D surface, I may need to adjust something, didn't have time to play with that.

Maybe easier to get better color on the 3D plot if I play it for longer or use gnuplot or other software / python libraries, you can try to explore yourself. Just google for "origin free alternatives", you'll see programs including veusz that I used, scidavis/alphaplot, and many more.

作者
Author: 12313 时间: 2024-7-7 10:36
本帖最后由 12313 于 2024-7-7 10:51 编辑

student0618 发表于 2024-7-7 00:45
I used the free (and open-source) software veusz to plot your data provided in another thread "使用g ...

Thank you very much.I'll google for "origin free alternatives" later. By the way,when I use command "gmx sham", if I should extract datasets of rmsd-rg.xvg after RMSD achieve equilibrium by using option -b ?

作者
Author: student0618 时间: 2024-7-8 10:38

12313 发表于 2024-7-7 10:36
Thank you very much.I'll google for "origin free alternatives" later. By the way,when I use comman ...

Yes, only that part is meaningful for studying equilibrium properties.

作者
Author: 12313 时间: 2024-7-8 11:38

student0618 发表于 2024-7-8 10:38
Yes, only that part is meaningful for studying equilibrium properties.

Thank you very much

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