OZGE ENGIN wrote:
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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