[gmx-users] Ion-Clustering?

[Mark Abraham]

On 8/01/2011 12:56 AM, Micholas Smith wrote:
> 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.

That's weird. What's your .mdp file?

Mark
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