i have the trajectory but i want to specify the atoms number to do the g(r)
recommendation procedure is here,
1: export final result(all atomic coordinate[xyz]) by VMD plugin: https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html
2: create a tool for calculate Radial Distribution Function. like a this one,
http://www.pages.drexel.edu/~cfa22/msim/codes/rdf.c
(description of method is here, http://www.pages.drexel.edu/~cfa22/msim/node28.html#eq:md:ungr )
3: execute RDF calculation tool by your data.
then, you can obtain good enough result. I think.
Have a good day!
A number of programs such as cpptraj in Amber, gmx tools, tinker modules can do this better than vmd, although the command line in vmd can do this efficient.
In the GUI panel of vmd, choose the analysis tools and you can find the rdf analyzing module.
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