Hello, I have done simulations on cyclic peptide nanotubes and trying to calculate the atomic concentration in the x and y axis, to measure the diameter of the tube. I have tried using the g_rdf, but the results are confusing to interpret. Here is the steps which I followed,
1. using trjconv, rotational and translational motions are removed from the centered trajectory. 2. and then, g_rdf -f trj.xtc -s ref.gro -n index.ndx -o out.xvg (I understood that the "-rdf atom" option is the default one and this will calculate the atomic distribution in the x and y plane) I am not sure whether the elimination of translational and rotational motions is enough to calculate this property, should I have to align the structure in the z axis using the PCA analysis? Regards, Raj.
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