<div dir="ltr"><br><div class="gmail_quote">On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek <span dir="ltr"><<a href="mailto:ondrej.marsalek@gmail.com">ondrej.marsalek@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear all,<br>
<br>
I would like to understand better the way g_rdf performs<br>
normalization. I have two unexpected results:<br>
<br>
1) In a simple simulation of atomic ions in water in a cubic box, I<br>
get RDFs that clearly reach a constant value at large enough<br>
distances, but that value is somewhat lower than one. The simulation<br>
is NpT, could that be a problem for the normalization?<br>
<br></blockquote><div>g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure water.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2) In a simulation in a dodecahedron, I get an unexpected decrease in<br>
the RDF at larger distances (for free ions in solution). Is there some<br>
know problem with normalization in triclinic cells? Is the RDF perhaps<br>
not truncated "soon" enough?<br></blockquote><div>Try calculating it for much larger distances, if you have PBC this should not be a problem even with the current docecahedron.<br><br>--Omer.<br></div></div><br>
</div>