[gmx-users] rdf doesn't tend to unity

David spoel at xray.bmc.uu.se
Mon Sep 12 14:06:33 CEST 2005

On Mon, 2005-09-12 at 13:31 +0200, Ester Chiessi wrote:
> Hi.
> I calculated the MD of a polymeric network in SPC water. I was very 
> surprised when I found that the rdf between the oxygen atoms of the polymer 
> and the water oxygen atoms doesn't reach the value of 1 at high r values.
> The g(r) remains lower than unity and tends to 0.87.
> I could expect a value higher than 1, eventually for inhomogeneity, but not 
> lower.
Test whether the integral (4 pi r^2 g(r)) goes to #Ow
Test whether the RDF goes to distances longer than half the shortest box
> Can this result have a physical meaning or is it an artifact?
> If there is a lower density at long distances, respect to the average 
> density in the system, it should be some r interval where g(r) becomes 
> higher than unity. Is it correct?
> I used pbc=full for the trajectory calculation, as polymer chains are 
> covalenty linked to their periodic images.
> Thanks in advance for any suggestion or comment.
> Ester 
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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