Dear Mary,
This is a very open question and not a very clear one.
I presume you are talking about a system with two solute components that
interact (bind), i.e. two proteins or a protein and a ligand, for example?
And what exactly do you mean by 'binding stability'?
The simple answer would be 'yes', as any starting condition, such as the
starting coordinates of ions, will cause a difference in the MD trajectory
obtained. And unless you look at properties that will be thoroughly sampled
in the time of your simulation (which are few properties of typical
interest, and almost certainly not the possible conformational sampling of
two solutes with respect to each other), you will get different answers
from different MD trajectories.
Maybe this helps...
If your question is more about a specific issue, then please rephrase it
accordingly.
--Marc
On 11 June 2013 09:27, Mary Varughese <maryvj1985.gmail.com> wrote:
> Sir,
>
> does the spatial arrangement of counterions around a complex affect the
> binding stability of the system during the production dynamics.
>
> Thanking you
>
> Mary Varughese
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Received on Tue Jun 11 2013 - 02:00:03 PDT
