[gmx-users] rdf problem

[Antonia V.]

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
 		 	   		  
Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. 		 	   		  
_________________________________________________________________
Hotmail: Powerful Free email with security by Microsoft.
https://signup.live.com/signup.aspx?id=60969
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100310/2cc4393c/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ATT00001
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100310/2cc4393c/attachment.ksh>