From: David A. Case <>
Date: Mon, 30 Apr 2007 08:24:34 -0700

On Mon, Apr 30, 2007, Sophie Barbe wrote:
> I minimized two conformational states of a protein in explicit water and in
> explicit octane. I compared the energies differences between the two states d
> (Estate2-Estate1) for the two solvent environment. For this, I noted the energy
> at the end of the output file.
> 5000 -3.5409E+03
> In octane solvent, the energies values are much more weaker than in water (1
> kcal / mol against 10 kcal / mol). Why such a difference???

There is no way of telling from the information you provide. The result
doesn't sound unreasonable. But just looking at the total energy of a
solvated system after minimization is not a very useful thing to look at.
You probably need to look at some free energy simulation (such as umbrella
sampling, or MM-pbsa) in order to average over the solvent configurations.

I know this is not much direct help, but it sounds like you may be trying to
get a too-simple answer to a more complex problem.

....good luck...dac

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Received on Wed May 02 2007 - 06:07:17 PDT
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