AMBER Archive (2004)

Subject: Re: AMBER: intramolecular energies

From: David A. Case (
Date: Tue Sep 28 2004 - 12:11:57 CDT

On Tue, Sep 28, 2004, Guanglei Cui wrote:

> What I want to calculate is the cohesive energy of some organic liquid,
> not pairwise decomposition energies. Also I'd prefer to having it
> calculated during an MD run, not postprocessing.

I think you should do this: take the average total potential energy for the
liquid, and divide by the number of molecules. Then, you will have do a
separate calculation for a _single_, gas-phase molecule. Subtracting these
should give you an estimate of the enthalphy of vaporization (if you include
some corrections for pressure-volume terms). A detailed description of this
process is given here (among many other places, I am sure):

%A H.W. Horn
%A W.C. Swope
%A J.W. Pitera
%A J.D. Madura
%A T.J. Dick
%A G.L. Hura
%A T. Head-Gordon
%T Development of an improved four-site water model for biomolecular
simulations: TIP4P-Ew
%J J. Chem. Phys.
%V 120
%P 9665-9678
%D 2004

(See esp. Eq. 19. If you don't have a polarizable force field, the correction
term "C" is pretty small.) Then you can roughly say:

    Delta H(vap) = <Ugas> - <Uliquid>/N + RT

(But see the above reference for additional corrections). If you need a free
energy of transfer from liquid to vapor, (and not just an enthalpy), you will
need to carry out much more extensive calculations.

...hope this helps...dac
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