AMBER Archive (2008)

Subject: Re: AMBER: Is boiling point a good way to validate solvent paramters?

From: David A. Case (
Date: Fri Feb 15 2008 - 20:49:12 CST

On Fri, Feb 15, 2008, Mike Wykes wrote:

> I did a quick calculation of the enthalpy of vaporization
> using the average potential energy (EPTOT in the md output file) in the
> equation Delta-H(vap) = -<U>/N + RT and got values completely different
> to experimental values. I then read the reference you sent me ( J. Chem.
> Phys.V 120, P 9665-9678) and realized that it was the average
> intermolecular potential energy that I was supposed to be using,

Actually, you should compute the average potential energy in the gas phase
(in a separate calculation) and subtract that from <U>/N in solution. For
small *rigid molecules* (as I believe I mentioned before) there is no gas-phase
MM potential energy, but this is not true for floppy or larger rigid solvents.
So, you are really doing a (solution - gas) calculation. The internal
energies are probably similar in the gas phase and in solution, but you should
not assume that they are exactly the same. See the papers cited earlier.

> On that note, how do I go about tweaking the benzene parameters? If I
> want to get an enthalpy of vaporization value close to the experimental
> value, my average intermolecular potential energy per molecule is going
> have to change from -12.8 Kcal/mol to around -8.7 Kcal/mol. I can either
> increase the positive and hence repulsive electrostatic interactions by
> scaling the charges or play around with the VDW constants to weaken the
> negative attractive VDWs interactions or do a combination of both.

The general procedure for Amber is to keep the charges fixed to the RESP
values, and only vary the Lennard-Jones parameters to get densities and heats
of vaporization correct. This is somewhat arbitrary, and results depend on
how much you have to change the 6-12 parameters to get good results.


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