On 2011-03-31 19.11, Elisabeth wrote:


On 31 March 2011 12:58, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:



    Elisabeth wrote:



        in your mail:


        On 30 March 2011 15:30, Justin A. Lemkul <jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@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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