[gmx-users] Counter ion and PME
David van der Spoel
spoel at xray.bmc.uu.se
Sat Mar 24 11:07:38 CET 2007
Tsjerk Wassenaar wrote:
> Personally, I rather add ions up to physiological salt concentration,
> in addition to counterions, which makes the equilibration quicker,
> also accounts for the presence of both positive and negative charges
> on the protein surface and, probably mainly due to the latter, has a
> stabilizing effect on the proteins in simulation.
Not meaning to be cynical but where does this wisdom come from? It makes
sense and most people will agree, but are you aware of any systematic tests?
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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