Re: pH in NAMD

From: Mark Abraham (
Date: Thu Feb 08 2007 - 19:12:40 CST

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.


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