[gmx-users] The system setup

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 28 06:43:55 CEST 2009

Chih-Ying Lin wrote:
> Hi
> I am going to simulate the lysozyme with some ligand in the low ionic
> strength phosphate buffer .
> The buffer condition will be
> (pH 7.2, 8.3 mM)  and (pH 5.0 ,  8.3 mM)
> For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water
> model and use CL- ions to nutralize the lysozyme (+8)
> and cationic ligands.
> Does my setting make sense?

It makes sense, but it doesn't model those buffer conditions. Calculate 
how many H+ you'd need in your simulation cell for pH 7.2. Likewise the 
phosphate species.

> Do you have any suggestion about this ?

Consider the titratable residues when trying to model a system at a 
different pH.


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