[gmx-users] how to calculate the conc in the genion
lina.lastname at gmail.com
Fri Aug 12 05:16:41 CEST 2011
On Fri, Aug 12, 2011 at 8:08 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 12/08/2011 2:22 AM, lina wrote:
>> On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar<tsjerkw at gmail.com>
>>>>> I'd be amazed if the error was in the code and not in your calculation.
>>>>> number of water molecules doesn't matter for the calculation of the ion
>>>>> concentration, of course. Pay attention to your box shape. And do
>>>>> the number of ions has to be an integer, so for a given volume you
>>>>> 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.
Thanks, I should not have used total number of ions.
>> 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
>>> 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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