[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:
>
>
>
> 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 ...
>
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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