[gmx-users] Heat of vap

[David van der Spoel]

On 2011-03-31 18.52, Elisabeth wrote:
>
>
> in your mail:
>
> On 30 March 2011 15:30, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     Elisabeth wrote:
>
>         Dear all,
>
>         I intend to obtain vaporization heat per volume for a /pure
>         alkane system/.  Here is the steps I am taking. Please correct me.
>
>         1- Obtain total energy of system (kinetic+potential) and divide
>         by number of molecules to obtain energy per mol of molecules.
>         g_energy -f *.edr -nmol XXX
>         2- Obtain total energy of a single molecule (use pbc).
>         3- Subtract step 2 from step 1.
>         4- Divide by simulation box volume.
>
>         My questions is:
>
>         in step 2 : what should be the box size? The same size as in 1
>         or it does not matter? (step 1 is done for the actual denstiy)
>
>
>     More troubling, how does one define the energy of a molecule?  If
>     you use any sort of long-range algorithms (especially PME, but also
>     dispersion correction), you can't simply decompose the system like this.
>
> Thanks Justin and David.
>
> I have been trying to find the article in which this has been presented.
> If you have time Please see page 5937, right column, equation 11. I
> think I made a mistake and I dont have to include kinetic energy, Only
> nonboded energies!?
Either Epot or Etot. It does not matter if you simulate at the same 
Temp. You could also consider using the enthalphy (gmx 4.5 and higher).
>
> http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539
>
>     In the derivation of recent Gromos96 parameter sets, the heat of
>     vaporization is quite simple:
>
>     DHvap = <Ugas> - <Uliq> + RT
>
>
> 1- So <Uliq> is the total energy or only potential (no kinetic)
> 2- How can I compute <Ugas>? I have liquid now...
>
>
>         Thank you,
>         Regards,
>
>
>     --
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>
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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