Dear all,
I am simulating a binary system of two non mixing components (5CB and water
using version 4-0-3; the whole equilibrated trajectory is about 300ns).
I want to calculate the rdf of the centers of mass of 5CB using the command
g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -noxvgr.
The problem is that the rdf I am getting does not approach one at long
distances. Is there a way to correct that?
I have the same problem, with all rdfs, and also when I compute the rdfs for a
lipid bilayer (DPPC-water)... I think it has to do with the way that the
normalization is done,
because the ones that are calculated for a one component system (i.e. bulk 5CB)
are normal (they do approach one).
Thank you,
Antonia
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