[gmx-users] rdf problem

Erik Marklund erikm at xray.bmc.uu.se
Tue Mar 9 10:39:01 CET 2010

Antonia V. skrev:
> 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 zero at 
> long distances. Is there a way to correct that?
> Thank you in advance for your help,
> Antonia
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But it should not, should it? The rdf normally approaches one for long 

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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