Dear all,
I would like to plot radial density curve for my spherical lipid system. I have plotted RDF graph using gromacs utility g_rdf as shown below:
gmx rdf -f traj.xtc -s topol.tpr -n index.ndx -o rdf.xvg -cn rdf_cn.xvg -bin 0.05 -com
How to post-process the output (rdf.xvg or rdf_cn.xvg) to get radial density plot (1/nm^3 vs nm)?
Thank you.
Venkat, such as I understand your question you have data Density/Radial size vs Radial size. If you divide Radial Size by its maximum value then the X axis would be between zero and unity. Graphs that result might be compared then. Does this help or am I missing some key spect?
Dear Sir,
Thanks for the quick reply. Gromacs rdf plots number density (g(r)) vs radial distance (nm). But I want to plot 1/nm3 vs radial distance (nm). How can I achieve this?
If that means that you have a function Y=1/x3 as a theoretical hypothesis, then you may plot the mathematical values of Y vs X for x>0. And if you have datasets with variables X,Y, you may study this third function Y=1/x3 from real data, measure its media, and make other analysis to compare empirical results with the theoretical ons. Is it the purpose of your research?
Hi! did you solve the problem? I'm trying to do the same thing, but I do not know how I have to transform g(r) (from the g_rdf) to radial density...
could you help me please?
thanks in advance
Hi,
Now you can plot radial density using gmx rdf tool, which is available in developmental version of Gromacs-5.2. You can get the same from github/gromacs.
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