# Re: pH in NAMD

From: Jan Saam (saam_at_charite.de)
Date: Thu Feb 08 2007 - 11:21:02 CST

Richard,

pH6 is not 10^-6 H3O+ particles per liter but rather

10^-6 mol of H3O+ ions which just 23 orders of magnitude more ;-)

However there would be "no" ion in your box anyway.

Jan

Richard Wood schrieb:
> 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...)
>
> Richard
>
>
>
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> rwoodphd_at_yahoo.com
>
>
> ----- Original Message ----
> From: Mark Abraham <mark.abraham_at_anu.edu.au>
> To: namd-l_at_ks.uiuc.edu
> Sent: Thursday, February 8, 2007 7:20:06 AM
> Subject: Re: namd-l: pH in NAMD
>
> > Hi
> >
> > Is it possible to change the pH in system for a NAMD simulation besides
> > changing the state of the acids/base amino acids residues?
>
> So if you wanted a pH of 6 in an explicit solvent MD simulation, say, how
> many hydronium ions would you have per simulation cell, and which physical
> model would you use?
>
> Mark
>
>
>
> ------------------------------------------------------------------------
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```--
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de
```

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