[gmx-users] rdf problem

Antonia V. antonia_haha at hotmail.com
Wed Mar 10 16:18:00 CET 2010

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,
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