[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.
> 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
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
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