Re: pH in NAMD

From: MW Van der Kamp, School of Chemistry (
Date: Fri Feb 09 2007 - 02:48:48 CST

Although the discussion of how best to calculate the number of H3O+ ions in
a certain volume at a certain pH is a nice one (brings us back to our basic
chemistry roots...), I would like to point out that you have to keep in
mind that adding H3O+ ions in a MM representation wouldn't actually do
anything with the 'pH' of the system. So even IF you would have such an
enormously large waterbox or extremely low pH that theoretically, you would
need to add H3O+ ions tp your system, they would be more or less equivalent
to 'normal' positive ions (like Na+) and simply add to the charge in your
system. (The MM description doesn't allow proton transfer from H3O+ of
So, as said before, if you want to simulate at a certain pH, a better way
(THE way with normal MM?) is to recalculate the protonation states of your
amino acid side chains at that pH.....


--On 09 February 2007 12:12 +1100 Mark Abraham <>

> 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!!!
> A simple and general way to look at this is to observe that pH 6 is 1e-6
> mol L^-1 is 1e-33 mol A^-3, and using Avogadro's number, is 6.022e-10
> atoms per cubic Angstrom. So to just get *one* H3O+ ion into a cubic box,
> you'd need a side length of at least 8000A. Even pH 1 is going to be out
> of the ordinary scale of MD simulations.
> Mark

Marc van der Kamp, PhD-student
School of Chemistry, Research group of Dr. Adrian Mulholland
University of Bristol

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