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.
In the derivation of recent Gromos96 parameter sets, the heat of vaporization is
quite simple:
DHvap = <Ugas> - <Uliq> + RT
I have seen this equation used in a number of other studies, as well.
-Justin
Thanking you all,
Regards,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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