[gmx-users] pH

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 21 03:49:48 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.

Try thinking about this problem realistically. You have a simulation 
volume that's something like a cube with side length of few tens of nm. 
Do some numbers and work out what order of magnitude of such cubes you'd 
need to have one H3O+, so as to correspond to a 
experimentally-measurable non-seven pH.


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