[gmx-users] electrostatic interactions

[XAvier Periole]

On May 3, 2010, at 6:40 PM, abdullah ahmed wrote:

> Actually I'd just like to know why both structures have such similar  
> coloumb energy values.
> If an electro-static interaction is being made in one structure and  
> not in the other then their coloumb energy values should be  
> different too, no? Wouldn't this be visible with simple energy  
> minimisation?
How different are they?

You mention you use encad with "full solvent". Does that mean you ahve  
the protein
solvated in a box of water?

If your point is only to show that in one case you have an  
electrostatic interaction and not
in the other you might just need to show that with an image! The  
energies after minimization
are not necessarily more meaningful ...

> I would prefer to not do molecular dynamics, because the structure  
> is biologically optimal in this conformation and molecular dynamics  
> may move it too much.
>
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