Re: [AMBER] Methane with no surface area?

From: David A Case <>
Date: Thu, 16 Jun 2011 15:00:02 -0400

On Wed, Jun 15, 2011, Christoph Klein wrote:

> I was running a simple single-point energy calculation on a methane molecule
> using GB implicit solvent to understand the solvation of small molecules. I
> found that the surface area contribution to the energy (ESURF) was 0
> according to the outputs. This was not the case for larger molecules such as
> ethane. What is the cause of this result and is it intentional?

This *may* be a weird consequence of the LCPO approximation used to get
surface energies. One would need to print out each contribution to the
total, to see how things work. Note tha the LCPO model is not a universal
one; rather it was parameterized on "ordinary" organic molecules.

You could try a single-point run with gbsa=2 to see what happens as well.


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Received on Thu Jun 16 2011 - 12:30:03 PDT
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