[gmx-users] Re: pKa calculations using gromacs

sameer varma varma1 at uiuc.edu
Fri Sep 10 16:36:31 CEST 2004

At 02:10 PM 9/10/2004 +0200, you wrote:
>On Fri, 2004-09-10 at 13:39, Markus O Kaukonen wrote:
> > Thank's Shameer for the nice reference.
> >
> > However, after reading the article two issues are still unclear to me
> >
> > 1) In
> > >Simonson, T., J. Carlsson, D.A. Case. 2004. Proton binding to proteins:
> > >pK(a) calculations with explicit and implicit solvent models. J Am Chem
> > >Soc 126(13):4167-80.
> > they do thermodynamic integration
> > from system A (protonated Asp) to system B (ionised Asp).
> > They use periodic boundary conditions and explicit water molecules to fill
> > the simulation box around protein (and within protein).
> > They add counter ions to neutralise the box in state A.
> > It is not said in the article if they add one more conter ion to state B.
> >
> > Question:
> > Is this really possible?
> > In one system (say A) they have
> > total charge of 0 in the system (after adding counter ions)
> > , but in B they have either total charge -1
> > (or they have added one more Na+ in the system which is not said in the 
> text).
> > Does not one run into troubles with electrostatistics when the simulation
> > cell is not neutral (authors have used Charmm and Amber).
> >
> > On the other hand, if one would add one more counter ion to state B
> > (to make its charge 0) this would add up uncorrect energy terms to state
> > B.
> >
>I suggest you contact David Case, he usually knows what he's doing, but
>as you describe it here it is fishy indeed.
>And of course you could contact Andre Juffer

You have raised quite an issue here but I would rather refrain from 
commenting on someone else's work. I am sure the authors must have thought 
out the simulation procedure carefully. And David is right about contacting 
the authors directly. That would avoid any unnecessary confusion.

cheers - sameer.

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