[gmx-users] pH

David van der Spoel spoel at xray.bmc.uu.se
Sun May 20 20:59:45 CEST 2007

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 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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