[gmx-users] electrostatic interactions

XAvier Periole x.periole at rug.nl
Mon May 3 19:11:08 CEST 2010

On May 3, 2010, at 7:01 PM, abdullah ahmed wrote:

> I wish I could use a picture :)
> Unfortunately, this is not possible since I need the energy value to  
> be able to compare this to other mutations of the same structure and  
> to provide a "measure" of how energetically favourable one is in  
> comparison to the other.
Ok, that is what I was suspecting ... then you should be really  
careful in using the minimized
energy as a "measure" of the different effect of the mutations in  
protein. This has probably
not much value!
You'd need to go to the free energy and not the enthalpy (potential  
energy) of one minimized frame
> And I am using a box of water because I feel that provides a better  
> estimation of natural conditions than a vaccum :)
In that case I am afraid the water should be relaxed ... equilibrated  
if you prefer.
Its interaction with the protein is probably no-sense. A minimization  
is not
sufficient to fix it.

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