# Re: pH in NAMD

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Feb 08 2007 - 09:58:50 CST

On Thursday 08 February 2007 10:36, Richard Wood wrote:
> Hi Mark,
>
> If, theoretically, your pH was 6, you'd have 1 x 10^-6 H3O+ ions per liter
> of solution. So, you'd need to know what the volume of your simulation
> was, i.e., how many liters (a really small number), meaning you'd have much
> less than 10^-6 H3O+ ions in your simulation!!!
>
> For example, I have a box of water that is 24A per side, which is a volume
> of about 13824 A^3. One 1 liter is 1000 mL, or 1000 cm^3. Conversely, 1 A
> is 1 x 10^-8 cm, so 1A^3 is 1 x 10^-24 cm^3. My box of water is therefore
> 1.3824 x 10^-20 cm^3. This turns out to be 1.3824 x 10^-23 L. Thus, I
> should have 1.3824 x 10^-29 H3O+ ions in my box to have a pH of 6. I'd
> obviously need to simulate a very large box in order to have the right pH,
> as my 24 A box of waters had 512 waters. I'd need to have a box of 3.7 x
> 10^31 waters in order to have ONE H3O+ for me to simulate.
>
> (I think I did the chemistry math correctly...)

No you didn't :-) although you do get the qualitative conclusion right. Think
about the order of magnitude again. 10^-29 molecules? Does this sound right?

Jerome

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