On Wed, Feb 13, 2008, Mike Wykes wrote:
>
> I am investigating the conformation of a molecule in both explicit
> benzene (BNZ) and acetronitrile (ACN) solvent boxes. Experimental work
> has shown the change in conformation to be dependent on the polarity of
> the solvent. Before doing md with my molecule in the solvent, I wanted
> to check the solvent was accurately described by the force field (GAFF)
> and that the charges I used are reliable.
>
> I obtained the charges for each solvent from the RESP database (
> http://q4md-forcefieldtools.org/REDDB/index.php ) project number W-46
> and then used Antechamber to read in the charges and assign the GAFF
> parameters.
>
> After initial minimization of the box that leap generated, and NVT
> temperature equilibration from 0-300K I ran a 2 ns NPT MD to equilibrate
> the density (with SHAKE turned on, dt = 0.002). I obtained a reasonable
> match to the experimental values: For ACN a density of 0.71 g/cm^3 at
> 300K (experimental value is 0.78 at 293K) while for BNZ I got 0.84,
> close to the experimental value of 0.88.
I would actually be a little concerned that the densities are so low -- this
might be a signal that the vdW parameters need to be tweaked.
What one usually checks for energies is the enthalpy of vaporization, which
can be computed easily from the average total potential energy per molecule
of a liquid calculation at ordinary temperatures. Getting this right helps to
ensure that the attractive forces holding the liquid together are about right.
>
> Then I tried to check the boiling point. I restarted the 300K MD run in
> NPT, but adding a restraint on the temperature so that it varied from
> 300K to 400k over 2ns. I kept SHAKE on, but reduced the time step to
> 0.001.
> Plotting the density as a function of time (and hence temperature) I
> expected to see a linear decrease up to the boiling point, then a
> sharper decrease in the density as the liquid boiled. Ideally this would
> be at 355K for ACN 353 for BNZ . But when plotting the density vs time,
> the density decreased more or less linearly with increasing temperature
> and did not plummet at any point between 300 and 400K.
This is probably not a good way to get the boiling point, since it would take
a very long time for the phase equilibration to take place. A better way
would be to compute the free energy of disappearing a particle from the
liquid. This, combined with the (easily-computed) free energy of re-creating
it in the gas phase, would give you a free energy of vaporization. Then doing
a temperature scan would be more likely to work. But, as I indicated above,
go for the enthalphy of vaporization first, since it is almost as good, and is
*much* easier to compute.
See this paper for the full theory here:
%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
but note that most of the complicated corrections are small for rigid solvent
molecules. So, you can start with just
Delta-H(vap) = -<U>/N + RT
Where <U> is the average potential energy, N is the number of solvent
molecules. (The "polarization" correction can be important for polar
molecules like water, and maybe acetonitrile, less so for benzene. The
equation above will get you close, but the full theory is needed if you want a
very careful result.)
If you want to see how to get the vapor pressure and boiling point, check out
the second paper in this series:
%A H.W. Horn
%A W.C. Swope
%A J.W. Pitera
%T Characterization of the TIP4P-Ew water model: Vapor pressure and boiling
point
%J J. Chem. Phys.
%V 123
%P 194504
%D 2005
...good luck....dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | skype: dacase
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
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Received on Sun Feb 17 2008 - 06:07:11 PST
