Re: AMBER: total energy of solvation

From: David A. Case <>
Date: Tue, 22 Feb 2005 21:40:47 -0800

On Tue, Feb 22, 2005, Holly Freedman wrote:
> I would like to be able to calculate the total energy of solvation
> averaged over an MD trajectory, meaning the average total energy of the
> entire system solvated in explicit water, minus the average energy of
> the gas phase molecule.

I bet you are going to be disappointed with this exercise. What you will
get will be a total potential energy of the whole (solvated) system that has
large fluctuations and not much (if any) intrinsic meaning. Subtracting out
the gas-phase solute energy is not going to help much, at least in any way
that I can see (?). The result is certainly not going to be a "total energy
of solvation", at least in the way that this term is usually used.

Can you say more about what physical quantity you ultimately want to estimate?
Of course, maybe I am missing something here, but what you describe seems
like quite an unusual calculation....

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Received on Wed Feb 23 2005 - 05:53:00 PST
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