[gmx-users] Re: Enthalpy Confusion
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 11 22:18:10 CEST 2013
On 2013-06-11 21:57, Jeffery Perkins wrote:
>> If you are computing enthaply in the NPT ensemble, P is constant, and
>> is the applied pressure.
>> The "pressure" quantity calculated from the KE and the virial is not
>> the pressure. It is a quantity that when averaged over time is equal
>> the pressure. Only the average is meaningful macroscopically.
> Right, that's an easy one to miss but i don't think that's my problem here.
>> If you are computing enthalpy in another ensemble (which is possible,
>> though it may be harder to interpret) then you would use the average
>> pressure from this quantity
> I'm running in NPT and was calcaulating H from ave. P, ave. U and ave. V for
> the run
> while i understand that this doesn't exactly equal average H it should be
> close enough for me at this point, going back and redoing it with P set to
> the reference value (which the average hits with small fluctuations)
> the resultant H still doesn't line up properly for some example data:
> "pV, g_energy" V, m^3 pV, J pV, kJ/mol
> 442.42 1.46E-26 1.46E-18 884.07
> P = 1000 bar = 100,000,000 Pa
> and i see that my pV is around 2x g_energies pV, no values are scaled for
> the # of items in the box at this point, this is all for moles of the system
> i think that's alright though
You should not use pV from g_energy though, as Michael explained, rather
you need ref_p times <V>. This precludes that your system is in
equilibrium of course.
> View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009062.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
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