Distance Histogram as a bar graph

User discussions
1

GROMACS version: 2021.4-2
GROMACS modification: No
I have performed a MD simulation and obtained a distance histogram using gmx distance command. Does GROMACS have a command to change the distance histogram into a Gaussian kernel density graph, or a bar graph? I read some scientific articles back in 2012 on MD simulations, where the distance histogram can be rewritten in a bar graph. I am wondering if GROMACS has a command added to gmx distance to write the distance histogram as a bar graph?

2

Could you explain a bit more what you mean? Why would you like a bar graph (usually used for categorical rather than continuous data)? I’m quite sure that there is no direct way to make a kernel density estimator plot, but you could probably make it yourself in, e.g., Python, see Histograms and Density Plots in Python | by Will Koehrsen | Towards Data Science.

3

Thank you. I presented my data as a continuous set of data to biology experimentalists. They said, “they like the bar graph, instead”. I was just wondering if GROMACS has a command, but thanks for the link.

4

See if the -binw option does what you want (together with -oh). But it won’t be a bar graph, but rather a histogram with wider bins.

Then you can plot it in different ways of course.