On 2013-06-14 19:28, 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?
a bit messy but this is data from g_energy for the system with increasing
temperature (300 K-1000 K), and constant pressure of 1000 bar (so 100 000
000 Pascals):
Temperature Volume Enthalpy Potential Total Energy pV
Kinetic En.
K nm^3 kJ/mol kJ/mol
kJ/mol kJ/mol kJ/mol
299.914 14.7226 -1168.83 -2565.44 -1611.63 442.791
953.817
399.901 17.462 -339.795 -2080.31 -808.501 468.706
1271.81
499.898 21.0263 421.763 -1666.7 -76.8794 498.643
1589.83
599.899 25.1149 1088.79 -1348.14 559.718 529.07
1907.86
699.914 29.4219 1668.2 -1115.47 1110.46 557.733
2225.94
799.925 33.764 2184.31 -943.613 1600.39 583.922
2544
899.923 38.0865 2660.3 -809.572 2052.45 607.847
2862.03
999.931 42.2798 3101.56 -707.908 2472.17 629.383
3180.08
all uncorrected for the number of particles in the box (so Etot is in kJ/256
mol of particles)
when i use this data to get H myself i get:
H
kJ/mol
-725.32948
242.7114
1188.90386
2071.63498
2881.65838
3632.9828
4345.2573
5017.41396
again uncorrected for the number of particles in the box
Thoughts?
Your calculation seems correct. Which gmx version did you use?
The correlation between the numbers is almost 100% so there must be a
simple explanation.
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Dept. of Cell & Molec. Biol., Uppsala University.
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