[gmx-users] Counter ion and PME
leafyoung81-group at yahoo.com
Sat Mar 24 21:38:23 CET 2007
Tsjerk Wassenaar wrote:
> Hi David,
> Yes, there has been a paper reporting on this point. No I haven't
> analysed this with statistical rigour as you might have expected from
> me. If you want the paper, I can dig it up for you.
Please post it here as well. It shall be of "public" interest. Thanks.
> On 3/24/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Tsjerk Wassenaar wrote:
>> > Hi,
>> > 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
>> 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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