[gmx-users] Three-site model for acetonitrile

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Thu Feb 27 09:43:26 CET 2003

Hi there,

I have tested the new topology (using two "just-mass" atoms
and three dummyfied atoms) overnight in a 1ns MD after
The system is stable and runs without error. The density
has improved a little bit and is 745g/l (with last version
it was 740). Another point is that the avg pressure
came out to be only <0.5 bar. I will reduce tau_p to
get this closer to 1bar before I will further disscus the density
and the energies.

Once more I have to ask, how to calculate the DHvap from
the simulation. I have found a formula in the literature
but it's not quite logic to me. They give:

DHvap= (RT - DHideal/real) - U
DHideal/real is an expt. correction for the diffrence between
ideal and real gas. So the exp. in brakets gives us the
inner energy of the real gas. Hence the whole expression would
give DUvap. Why is there no +pDV?

Which value do I use for -U? From the belly I would use the
total energy of the simulation, but doing so I get very bad
agreement with the exp. values. On the other hand if
I use the potential energy it comes out almost perfect.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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