[gmx-users] Heat of vap

[Elisabeth]

On 31 March 2011 12:58, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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!?
>>
>> http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539
>>
>>
> What is cohesive energy and how does it relate to the quantity you're
> trying to calculate?
>
> It is delta Hvap/volume. It is directly related to Hvap. What is happening
> is that they are calculating nonbonded energy of some chains, divide by
> number of chains and substract from nonbonded energy of a single chain in
> vacuum. These are the steps I wrote in my first post but I think I should
> not have included kinetic and should just look at LJ-SR and Coulomb-SR.
>

I am using PME..If I remember correctly LR is included in Coulomb-SR and can
not get decomposed? But I dont think this doesnt matter since if I am to
take nonbonded energies this should not hurt,,,

Please comment ...



>
>>    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)
>>
>
> Potential.
>
>
>  2- How can I compute <Ugas>? I have liquid now...
>>
>>
> Run a simulation in the gas phase.
>

Sorry, but how can I do this? :( I have box of molecules with density of
actual liquid..How can I shift to gas phase ..I mean how many molecules I
need to keep in the box..

Many thanks...

>
> -Justin
>
>
>>        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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>>
> --
> ========================================
>
> 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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