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

lina lina.lastname at gmail.com
Thu Aug 11 18:22:13 CEST 2011

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.

Here if consider the water, certainly the water volumn will be greatly
smaller than the box volumn, so the concentration will reach very

I might be wrong in some way, hope someone can point out.


> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Best Regards,


More information about the gromacs.org_gmx-users mailing list