[gmx-users] how to calculate the conc in the genion
lina.lastname at gmail.com
Thu Aug 11 17:42:47 CEST 2011
On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>> 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.
> 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
I did another quick check, which regardless of my way of calculation.
two cubic box, the same conc.
I compared the ratio of Na+CL in two box is 24/60=0.4
while I compared the volumn ratio is 149.6/533.39=0.28.
This way is easily for others to check too. read the ions from two
topol.top and the dimension from two .gro.
> Hope it helps,
> 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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