[gmx-users] Re: Enthalpy Confusion

[David van der Spoel]

On 2013-06-11 23:31, Jeffery Perkins wrote:
>>> or should i be doing < U+<V>*ref_p > = <H>?
>
>> More specifically, <U> + <V>*ref_p = H
>
>> <H> isn't really meaningful thing.  I mean, you can define something
>> such that <H*> = H, but that's not really thermodynamics.
>
> sorry I always have issues deciding how to talk about this stuff, so thanks
> for putting up with my terrible notation =)
>
>>> example system gives <H> = -1168 kJ/mol and i find <H> = -725 kJ/mol
>>> either
>
>> Interesting.  What material at what phase conditions?  For liquids,
>> the PV contribution should be very small.
>
> I hadn't really thought about that... but the system is a monatomic
> Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass =
> 40 amu) which should be a liquid at the conditions I was looking at, P=1000
> bar, T = 300 K using phase diagram in: Equation of state for the
> Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37,
> No. 5, 1429-1454
>
> the <U> is -1600 and the p<V> is 880 when manually done, around 400 from
> g_energy
Here's the code:
             /* This is pV (in kJ/mol).  The pressure is the reference 
pressure,
                not the instantaneous pressure */
             pv = vol*md->ref_p/PRESFAC;

             add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
             enthalpy = pv + enerd->term[F_ETOT];

What is your volume?
What is Etot?

PRESFAC  ~ 16.6




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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se