[gmx-users] Re: pKa calculations using gromacs

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 10 14:10:06 CEST 2004

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


More information about the gromacs.org_gmx-users mailing list