[gmx-users] Three-site model for acetonitrile

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 27 16:30:50 CET 2003

On Thu, 2003-02-27 at 09:43, Christoph Freudenberger wrote:
> Hi there,
> I have tested the new topology (using two "just-mass" atoms
> and three dummyfied atoms) overnight in a 1ns MD after
> equilibration.
> 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

U is the potential energy 
U = Einter(l) + Eintra(g)

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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