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

[lina]

On Thu, Aug 11, 2011 at 10:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 12/08/2011 12:37 AM, lina wrote:
>>
>> Hi,
>>
>> after using genion -conc 0.1
>>
>> certain number of Na and Cl were added in solvent.
>>
>> but when I tried to calculate back, namely, based on the number of Na
>> and Cl, the number of water molecular and the box volumn,
>> but seems can't come back, I mean, can't obtain the result of 0.1mol/L.
>>
>> I read the manual, "...the specified concentration as computed from
>> the volume of the cell..."
>>
>> the cell? Has anyone tried to calculate the concentration back?
>>
>> ( I guess might the way I calculate was wrong? the Avogadro's Constant
>> = 6.0221415 в 10^23 mol-1)
>
> 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.

I did use the box volumn first, but a bit far away from it.

so I wonder whether it means the concentration of the solvent involved,

another concern, what if the cell has large area no water, so how the
concentration calculated, still the whole box?

Thanks,
>
> Mark
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-- 
Best Regards,

lina