[gmx-users] Ion-Clustering?

Erik Marklund erikm at xray.bmc.uu.se
Sat Jan 8 21:46:15 CET 2011

Clustering of ions has been seen before. It is for instance discussed in 
Hess, B. et. al. J. Chem. Phys. 124, 164509 (2006).



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
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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