[gmx-users] Heat of vap
katesedate at gmail.com
Thu Mar 31 18:52:54 CEST 2011
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul <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
>> 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
> 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,
> 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
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