I want to plot the time serie data of number of hydrogen bond (between protein-ligand) from a MD simulation with Gromacs as in this picture:
http://igem.org/wiki/images/3/3e/Zju_model1_10.png
Instead of the classic Grace style.
https://www.researchgate.net/profile/Trevor_Marshall2/publication/305254443/figure/fig2/AS:391130341494799@1470264148666/A-plot-from-the-Gromacs-g-hbond-software-of-the-instantaneous-number-of-hydrogen-bonds.png
The first plot seems to come from R. Trie it, but all I could get is that:
R_hbond.PNG (see attached)
Using:
qplot(x, y, xlab = 'Time (ns)', ylab = 'Number of Hhonds', geom = c("path", "smooth"))
x : time
y: # h bonds (see attached file Lig_H_bond.txt)
Tried different geom options without success.
It would really nice if someone can help me out.
Thanks a lot!
I had a quick play with the data in Matlab because I thought I understood the problem. I'm not sure if you have access to that, but attached is the code that produced the figure.
I believe the problem to be the resolution on the x-axis. The plot you show on the Zju_model1_10 looks to have a significantly lower resolution (my guess is 1-ns).
Your data is 0.01-ns ?
I present 2 options to you. You either interpolate back, or average back to 1-ns resolution.
Or, if i am wrong about the resolution and your data matches, then in order to have the same look as Zju, you must zoom 100x.
I hope that helps.
Thank you for your replies.
Yeah Jamie you are right.
My data is 0.01-ns. The work-around I have found meanwhile is to plot every 1 ns which gives me the attached figure.
I don't have Matlab available now. Thank you for the code though.
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