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

David van der Spoel spoel at xray.bmc.uu.se
Sun May 20 22:39:26 CEST 2007

Dmitriy Golubovsky wrote:
>     From: David van der Spoel <spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>>
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto: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.
supposedly you know what you have in your system, and since you won't 
have any bonds breaking you can compute any concentration you like. 
since you most likely have zero H3O+ and zero OH- the pH is then that of 
a neutral system.
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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