If you have aggregation and a small box size, then the rdf will not be able to asymptote to one.
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Antonia V. Sent: Thursday, 11 March 2010 2:18 AM To: gmx-users@gromacs.org Subject: [gmx-users] rdf problem 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. <https://signup.live.com/signup.aspx?id=60969> ________________________________ Hotmail: Powerful Free email with security by Microsoft. Get it now. <https://signup.live.com/signup.aspx?id=60969>
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