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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 12 02:08:05 CEST 2011

On 12/08/2011 2:22 AM, lina wrote:
> On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar<tsjerkw at gmail.com>  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.
>> 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.
> Yes. I do agree with you.
> Here I have a field problem, I will be very glad if I can be told
> which part of calculation is wrong.
> a cubic box: Volumn = 101.57 *105.03 * 87.82 A  = 9.369E-25  m^3 = 93.69E-23 L
> total ions: 121
> so the concentration based on the box volume is:
> 121/AvagadroConstant/Volumn =
> 121/6.022E23/93.69E-23=121/6.022/9.369=0.214 mol/L?
> But before when I used -conc, the number I chose maybe 0.1 or 0.15
> mol/L, but not 0.2mol/L.

That's the concentration of total ions, but the concentration of each 
ionic species is about half that.


> Here if consider the water, certainly the water volumn will be greatly
> smaller than the box volumn, so the concentration will reach very
> high?
> I might be wrong in some way, hope someone can point out.
> Thanks,
>> 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
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
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