Re: [AMBER] Protein + Bilayer Simulations: Role of salt

From: Lalit Dubey <>
Date: Mon, 1 Mar 2010 08:43:48 -0600

Hi Jason,

Thats truly the way to think about the role of ions in a protein+Bilayer
simulation at first. Thanks. But whats the judgement or say, convention as
of now. We can think of a 'protein' as a generic one. Nothing especial. (All
polar residues are towards outside surface and hydrophobic ones
are buried inside). [Mine is pkc with +1e charge].

Whats the motivation for those who do protein + Bilayer simulations to add
or just to not add salt concentration in the system??

Mine was that it hardly matters in such a big system and contemporary others
are not treating it (as a critical factor) and still doing protein+Bilayer
simulations. Moreover, our experience with other similar systems shows
little effect on salt concentration.[I am going to write individually to all
those who have published such a work however I want initial motivation
factors that makes the judgement at first].

yeah, I have to address this question as raised in a seminar.

Thanks again,
--- Lalit

On Sun, Feb 28, 2010 at 6:40 PM, Jason Swails <>wrote:

> On Sun, Feb 28, 2010 at 6:35 PM, Lalit Dubey <>
> 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 Mon Mar 01 2010 - 07:00:03 PST
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