[gmx-users] pH

[Erik Marklund]

20 maj 2007 kl. 20.59 skrev 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.

Depending on your specific application, CPHMD can be used to simulate  
with constant pH. Unfortunately, CPHMD utilizes lambda-dynamics,  
which is not yet implemented in gromacs. It should not be THAT hard  
to implement yourself if you know a thing or two about MD and  
programing in general.

/Erik

>
> 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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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys