[gmx-users] problem with g_rdf

Yang Ye leafyoung81-group at yahoo.com
Sat Mar 24 16:14:22 CET 2007

> Hi,
> First of all, I wish, everything is o.k  for everybody  :) 
> I have a question about the g_rdf command. I read the mailing list but I could not find any problem simiIar to mine. I want to calculate the radial distribution function of my system which consists of  tripeptide and water molecules. In this respect, I select two groups: the peptide as the first and the water molecules as the second.Then I plotted the given rdf.xvg file, and what I saw was not an expected one. The distribution of particles increased with respect to increasing distance. I could not get the values of g(r ) on the y axis.   
You shall use xmgrace -nxy to view g_rdf's output.
>  The distribution did not show the first and the second peaks that correspond to the first and the second hydration shells, respectively. 
Sorry. You but not me shall answer this.
> What is the problem?
> Thanks in advance
> Ozge Engin
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