From: Richard Law (rlaw_at_llnl.gov)
Date: Thu Feb 08 2007 - 11:03:07 CST
The only sensible way to represent pH in a simulation of our size is perform
a pka calculation on your protein and choose sidechain ionisation states at
a different pH.
John Mongan did some cool constant pH stuff for Amber. i.e. the ionisation
states are allowed to change during the simulation.
Rich.
On 2/8/07, Richard Wood <rwoodphd_at_yahoo.com> wrote:
>
> Hi Jerome,
>
> Ok, I got the volume right, not the number of H3O+ ions. It's been a long
> time since I did any wet chemistry. And so, I forgot about Avogadro's
> number. The pH of 6 is 1 x 10^-6 MOLES of H3O+, and not MOLECULES of H3O+.
> Thus, I would need 6.022 X 10^23 * 1 x 10^-6, or 6.022 x 10^17 H3O+ ions
> in a liter, or 8.325 x 10^-6 ions in my box. of 512 waters.
>
> I would thus need a box 120122 times this, or a box of 61502884 waters to
> have a one H3O= ion and a pH of 6.
>
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> rwoodphd_at_yahoo.com
>
> ----- Original Message ----
> From: Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> To: Richard Wood <rwoodphd_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Sent: Thursday, February 8, 2007 10:58:50 AM
> Subject: Re: namd-l: pH in NAMD
>
> 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 3.7x
> > 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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-- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++YNWA Dr. Richard J. Law Biosciences & Biotechnology Division Chemistry, Materials and Life Sciences Directorate Lawrence Livermore National Laboratory L-372, 7000, East Ave, Livermore. CA. 94550 USA tel: +1 925 424 2338 fax: +1 925 422 4665 http://www.llnl.gov/bio/people/law/index.html ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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