Re: pH in NAMD

From: Mark Abraham (
Date: Fri Feb 09 2007 - 09:54:34 CST

MW Van der Kamp, School of Chemistry wrote:
> 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 course)
> 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.....

Yes, indeed... as implied in my original response-questions about the
physical model one would use for these waters and ions :-)

In a few decades, we may get to systems large enough that a real
dissociative water model becomes relevant for simulation!


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:22 CST