[gmx-users] Re: gmx-users Digest, Vol 37, Issue 73

Dmitriy Golubovsky dmitriy.golubovsky at gmail.com
Sun May 20 22:30:49 CEST 2007

> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Sun, 20 May 2007 20:59:45 +0200
> Subject: Re: [gmx-users] pH
> 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"?
> Dear David,
thanks for a quick answer.
1. what do you mean, when you say "pH is always seven".
2. when I said "dissociation", I mean that, I didn't use Morse potential for
the bond, so, for examle, COOH group haven't got probability to break the
connectivity with H atom.
3. i haven't got an idea how to calculate H3O+ concentration.


Dmitriy Golubovsky
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