Clustering of ions has been seen before. It is for instance discussed in
Hess, B. et. al. J. Chem. Phys. 124, 164509 (2006).
Cheers,
Erik
Micholas Smith skrev 2011-01-07 14.56:
Hello everyone,
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.
Thanks in advance.
Micholas D. Smith
Graduate Student
Drexel University
--
-----------------------------------------------
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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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