[gmx-users] ion contact: rdf does not tend to 1

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Thu Mar 29 00:01:15 CEST 2007

> I noticed that calculating the contact between the structural 
> ions in a protein with protein itself (the oxygen atoms 
> actually) the rdf does tend to 0 (at 6 nm it is 0.574 but it 
> seems going down) rather than 1. Could it be explained with 
> the fact the I am calculating the rdf on a non-homogeneous  
> situation?. In few words, after few nm there are not oxygen 
> atoms interacting with the ion.

Yes, that is typically the reason, it is an aggregated type of system,
with essentially no or significantly less atoms in the bulk.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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