# [gmx-users] Heat of vap

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 31 19:16:49 CEST 2011

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

PME energies are from nonbonded interactions.  The mesh energy is written to the
"Coul-recip" term in the .edr file.  If there is some other "Coul (LR)" term, it
is because you're using a twin-range cutoff such that rcoulomb > rlist, which I
do not believe is correct when using PME.

>
>
>
>            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..
>

Make a box with an equivalent number of molecules separated by some large amount
of space (i.e. 50 nm or so).  Set pbc=no and all cutoffs to zero.  I'm basing
this on Gromos96 parameterization, but I don't know what your target force field is.

-Justin

> 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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--
========================================

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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