[gmx-users] how to calculate the conc in the genion

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 11 18:23:55 CEST 2011

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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