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

[Ester Chiessi]

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.

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