[gmx-users] Heat of vap

[Elisabeth]

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
>> 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!?

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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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