[gmx-users] Heat of vap

[David van der Spoel]

On 2011-03-31 19.11, Elisabeth wrote:
>
>
> On 31 March 2011 12:58, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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> <mailto: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 ...
It is simple.
Compute Epot with all normal liquid options (PME, Dispcorr etc.).
Compute Epot for a gas phase molecule without any cutoffs
Apply equation below.
For OPLS/AA we obtain close to 98% correlation between experiment and 
simulation (paper submitted).
>
>
>             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> <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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se