Tsjerk Wassenaar wrote:
Hi,
I'd be amazed if the error was in the code and not in your calculation. The
number of water molecules doesn't matter for the calculation of the ion
concentration, of course. Pay attention to your box shape. And do consider
the number of ions has to be an integer, so for a given volume you cannot
get arbitrarily close to a given concentration.
The error is, to my humble opinion, in the reasoning. Concentration is
a macroscopic property, and when dealing with a minute volume, the
concentration of something in it is ill defined. Especially when
there's something else in that volume, taking up a significant amount
of space, like a membrane, protein or void, it becomes troublesome. I
would argue that the worst you can do in that case is take the volume
of the box and calculate the number of things to add from there to
reach a given concentration.
I'm wondering if you can elaborate a bit on this. I can understand your point
in the case of interfacial systems, membranes, or other biphasic systems, but
for a protein in water, why does the volume occupied by the protein matter? All
components - protein, water, ions - are all part of the same phase and
contribute to the total volume. Experimentally, one simply adds the desired
amount (either dry or from concentrated stock) and dilutes to the necessary
final volume. There is no distinction made for volume occupied by a protein,
substrate, or buffer component. Is this distinction really necessary in the
simple case of a protein in water? I'd be curious to hear your thoughts.
-Justin
Whether the number of water molecules matters for the calculation of
the ion concentration depends on the unit you use for concentration.
Probably molality is a better option than molarity. For that you do
take the number of water molecules. Frankly, that's what I usually do.
Doing so will give a desired concentration of ions in the solvent,
regardless of volume occupied by other (big) solutes or by nothing.
There is just one problem that stays nonetheless; in how far does the
bulk concentration you use as target correspond to the local
concentration you might need to use? Solutes, membranes and voids may
alter the local concentration significantly.
By the way, Lina, it would have helped if you had given the equations,
numbers and outcomes that lead you to believe there is something
wrong.
Hope it helps,
Tsjerk
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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