[gmx-users] how to calculate the conc in the genion
lina.lastname at gmail.com
Thu Aug 11 16:59:41 CEST 2011
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:
>> 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?
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