[gmx-users] pH

[David van der Spoel]

Dmitriy Golubovsky wrote:
> Dear Guru!
> 
> have you got any idea, on what how to calculate pH. for the system?
> i'm solving a promblem of coil-globule transition for polymer.
> do the topology for my structure(opls ff), do MD in water (spc). get the 
> statiscts. everything is ok.
> the summary charge is equal to zero. no dissociation.
> so the question is - how to calculate pH. or it's not possible?
> if it is possible, than how to variate this pH in some range.
> 
> I allready try to use genion, but didn't get good results, on case of 
> very big dependence of the results from the initial conformations of ions.
> 
How about computing the H3O+ concentration?
It is close to impossible to simulate realistic pH with limited size 
systems. In practice your pH is always seven.

What do you mean with "no dissociation"?

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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