On 2011-03-31 18.52, Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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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