On Sun, Feb 28, 2010 at 6:35 PM, Lalit Dubey <dubey.lalit.gmail.com> wrote:
> Hello Florent,
>
> Thanks for the quick response!
>
> Yes, indeed putting counter ions to neutralize the whole system is required
> for full PME calculation of electrostatic forces.
> This part is fine. I have added counter ions. My systems are neutral.
>
> My question concerns with the effect of *'physiological concentration of
> salt'* (say, NaCl) on the configuration of protein.
Maybe yes, maybe no. Depends on your system. Evaluating even
classical laws on that number of interacting particles is inherently
chaotic and with the right set of variables anything can happen.
Look for experimental data about your protein -- do they control the
salt concentration? Do they say what happens to the activity when
it's absent? Do they address it?
I'm guessing if you're looking to publish this data, a reviewer may
ask that exact same question, and the only way of addressing it really
is to run those simulations. But again, maybe not if salt is known
not to be a large factor. All-in-all, this is a very long non-answer.
That's my $0.02.
As a side note, when a system is not formally neutral, a "neutralizing
plasma". This is how, for instance, softcore potential TI is handled
when the net charge of the system changes (I'm pretty sure).
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Feb 28 2010 - 17:00:04 PST
