Hi,
I would like just notice that:
$molecules = 6.022 * 1220641.148*(0.1) / 10000 = 73.507 NOT
originally reported 734.722 molecules !
Another thing is that if one would like to use really precise
concentration, the volume reported by tleap/xleap/sleap
after solvatebox/solvateoct execution is not the right one.
The right volume of the box one may find on the end of the *.out file
of the sufficiently long equilibrating NPT run.
Speaking about the water and standard conditions the final (equilibrated)
volume of the box is approximately 1.15 times smaller than the initial
volume,
but if you need really precise number you have to do that equilibrating
NPT run.
Best,
Marek
Dne Fri, 31 Aug 2012 16:32:39 +0200 Daniel Sindhikara
<sindhikara.gmail.com> napsal/-a:
> Maybe I'm misreading your question but I think you answered it yourself.
> The formula apparently gives you the number of molecules, does it not?
> Perhaps you're looking for a different quantity?
>
> On Thu, Aug 30, 2012 at 9:30 PM, Carlos Romero
> <carlos.rom.74he.gmail.com>wrote:
>
>> Dear all
>>
>> I have a question regarding calculate the exact number of ions to reach
>> a
>> certain salt concentration.
>>
>> I have read in Amber mailing list that there is a perl script for this
>> purpose, but sincerely I do not know how to adapt it for my system.
>>
>> I have read perl script and I have found a line where calculate the
>> number
>> of molecules
>>
>> $molecules = 6.022 * $volume * $molar / 10000;
>>
>>
>> my question is: Is there any posibilty to use this relation in order to
>> calculate number of molecules?
>>
>> volumen of system is 1220641.148 A³
>>
>> molar concentration I need is 0.1
>>
>> applying this relation I get:
>>
>> $molecules = 6.022 * 1220641.148*(0.1) / 10000 = 734.722 molecules
>>
>> of course I would change volumen if needed in order to reduce number of
>> molecules
>>
>>
>> is it feasible or do I need run th script? please does anyone could
>> help
>> me?
>>
>> Regards
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Fri Aug 31 2012 - 08:30:02 PDT
