[gmx-users] Re: Enthalpy Confusion

[David van der Spoel]

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.

>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009164.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>


-- 
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