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Clustering of ions has been seen before. It is for instance
discussed in Hess, B. et. al. J. Chem. Phys. 124, 164509 (2006).<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
Micholas Smith skrev 2011-01-07 14.56:
<blockquote cite="mid:fb7aff25136db.4d26d526@drexel.edu" type="cite">
<div style="font-family: 'Times New Roman'; font-size: 16px;">Hello
everyone,<br>
<br>
I've been performing some rather long simulations (400ns) of a
short peptide chain in explicit TIP4P water solvent using
opls-aa forcefield with ionic concentrations near 1M, and I am
finding a lot of "clustering" of my ionic species. Has anyone
else run into this type of problem? I am running NPT with a
temperature of 283K with berendsen coupling. For electrostatics
iI am using PME, which I have been told works welll with ions in
solution. The clustering of the ions reminds me of a
crystallization process, this just doesn't feel like it's
physical.<br>
<br>
Thanks in advance.<br>
<br>
Micholas D. Smith <br>
Graduate Student<br>
Drexel University<br>
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<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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