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    The document discusses empirical energy expressions used in computational chemistry. It covers parameters for stretching, bending, torsion, and out-of-plane interactions as well as Columbic interactions and van der Waals forces. It also discusses solvation models, including implicit models that use Poisson-Boltzmann equations and explicit models like SPC and TIP3P. Visualization programs mentioned include VMD, Maestro, and GROMACS for calculations on Linux.

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    The document discusses empirical energy expressions used in computational chemistry. It covers parameters for stretching, bending, torsion, and out-of-plane interactions as well as Columbic interactions and van der Waals forces. It also discusses solvation models, including implicit models that use Poisson-Boltzmann equations and explicit models like SPC and TIP3P. Visualization programs mentioned include VMD, Maestro, and GROMACS for calculations on Linux.

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    5 views1 page

    2 Moljegyzet

    Uploaded by

    Nindzsák nindzsája
    The document discusses empirical energy expressions used in computational chemistry. It covers parameters for stretching, bending, torsion, and out-of-plane interactions as well as Columbic interactions and van der Waals forces. It also discusses solvation models, including implicit models that use Poisson-Boltzmann equations and explicit models like SPC and TIP3P. Visualization programs mentioned include VMD, Maestro, and GROMACS for calculations on Linux.

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    of 1

    +Empiriccal energy expression

    -parameters:streching, bending, torsion, 4th - out of plane


    -columb inteaction
    -wander vaals-|
    -in stacking connections -> in benzol ring
    -envirement - stackng is not the same we cant have a T shape!!!
    -halogenbond

    ++Energy expressions

    forecefield
    Morse type of potential

    U- totall energy = Kˇr (r-rˇeq)^2


    K - spring contstant
    bonds + angles + dihedrals + van der waals + electrostatic + improper
    diéterek - Vˇn / 2 (1+ cos [n 0| -epsilon(y)])
    Van der Waals -

    whats should i provide:


    - cordinates for the atoms

    -always check atom type

    ++Solvation I. - implicite models


    shielded interaction for the clumbic part
    pb equations
    permability eq.
    + new surface parameter

    adv.:

    ++Solvation II. : explicit models


    -Simplest model is: SPC - simple point charge or TIP3P model

    ----------------------------
    program to linux - GROMACS - calculations
    alredy have: VMD, maestro academic license
    maestro - linux - demsond - can be visual and

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