I want to plot g_rdf for peptide and SDS. In many papers I have read "*The
functions were normalized by the number of atoms in the first selection
(peptide atoms) and by a density of 0.01*".
1) I don''t find any option in g_rdf to normalize by density of 0.01.
There is one option -[no]norm*yes* (Normalize for volume and density) but
no option to put the value 0.01.
2) Does normalized by the number of atoms means to use the below option:
-rdf* enum* atom
RDF type: atom, mol_com, mol_cog, res_com or res_cog
Can anyone please explain.
I have included a link of the reference paper
http://www.sciencedirect.com/science/article/pii/S0005273606000940
Note that the figure legend says "arbitrary density" so they were probably just trying to plot values of similar magnitude. I don't know what value that has. There is no scaling factor available in g_rdf; one would simply post-process the RDF with some script (Perl, Python, etc) and apply scaling factors to those values. But again, I have never seen anyone do this before. Perhaps you should contact the corresponding author of the paper and inquire as to why they did this.
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