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    Fredrick Mutunga
    Molecular dynamics simulations allow us to model the movement of nuclei by considering them as classical particles moving according to forces derived from a potential energy surface. The position and velocity of nuclei are updated over small time steps using algorithms like Euler integration, Runge-Kutta, or symplectic integrators. Intermolecular interactions can be modeled using a supermolecule approach, which requires corrections like counterpoise to account for basis set superposition error. Excited electronic states can be calculated using methods that incorporate multiple Slater determinants, such as configuration interaction, coupled cluster theory, or time-dependent density functional theory.

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    BOMD Input

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    Fredrick Mutunga
    224 views26 pages
    Molecular dynamics simulations allow us to model the movement of nuclei by considering them as classical particles moving according to forces derived from a potential energy surface. The position and velocity of nuclei are updated over small time steps using algorithms like Euler integration, Runge-Kutta, or symplectic integrators. Intermolecular interactions can be modeled using a supermolecule approach, which requires corrections like counterpoise to account for basis set superposition error. Excited electronic states can be calculated using methods that incorporate multiple Slater determinants, such as configuration interaction, coupled cluster theory, or time-dependent density functional theory.

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    Molecular dynamics simulations allow us to model the movement of nuclei by considering them as classical particles moving according to forces derived from a potential energy surface. The position and velocity of nuclei are updated over small time steps using algorithms like Euler integration, Runge-Kutta, or symplectic integrators. Intermolecular interactions can be modeled using a supermolecule approach, which requires corrections like counterpoise to account for basis set superposition error. Excited electronic states can be calculated using methods that incorporate multiple Slater determinants, such as configuration interaction, coupled cluster theory, or time-dependent density functional theory.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    224 views26 pages

    BOMD Input

    Uploaded by

    Fredrick Mutunga
    Molecular dynamics simulations allow us to model the movement of nuclei by considering them as classical particles moving according to forces derived from a potential energy surface. The position and velocity of nuclei are updated over small time steps using algorithms like Euler integration, Runge-Kutta, or symplectic integrators. Intermolecular interactions can be modeled using a supermolecule approach, which requires corrections like counterpoise to account for basis set superposition error. Excited electronic states can be calculated using methods that incorporate multiple Slater determinants, such as configuration interaction, coupled cluster theory, or time-dependent density functional theory.

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    Molecular Dynamics

    Molecular Dynamics Simulation


    For electrons we have to solve the quantum Schroedinger Equation
    For nuclei we only consider that they move classically
    2

    d x
    dV

    F ma m 2 mx
    dt
    dx

    Force on nuclei can be obtained from potential derivative

    x t t x t x t t

    x t t x t x t t
    xt 1 dV
    m dx

    x t

    For example for harmonic oscillator

    Initial Condition: You give starting geometry and


    velocity then you calculate the force from your
    potential energy surface. Using the force you
    calculate the velocity and position change, then
    continue on.

    1
    2
    V x k x xeq
    2
    dV

    k x xeq
    dx

    Types of Force Fields used in


    Molecular Mechanics

    V V0 cosa

    12 6
    V x 4
    x
    x

    1
    2
    V x k x xeq
    2
    Wikipedia Molecular Mechanics

    On the fly simulation


    At every time step solve the electronic Schrodinger equation
    Good Points
    1. Accurate
    2. Can describe reaction
    3. Do not have to worry about fitting problems
    Bad Points
    1. Computational time is great so can only be used for
    short time propagation
    2. Can not perform detailed analysis

    Gaussian 09 BOMD input

    G09 BOMD output 1

    G09 BOMD output 2

    Method of Propagation1
    Goal:

    dx
    f x, t ; xt0 x0 xt final in time step t
    dt
    Euler method (first order method take gradient)
    xn 1 xn f xn , t n t

    4th order Runge-Kutta propagation : add up


    contribution along the way
    1
    xn 1 xn k1 2k 2 2k3 k 4 t
    6
    k1 f xn ,t n ;
    k 2 f xn 0.5k1t , t n 0.5t

    k3 f xn 0.5k 2 t , t n 0.5t ; k 4 f xn k3t , t n t

    Method of Propagation 2
    Predictor Corrector : repeated Euler
    x1n 1 xn f xn , t n t

    1
    1
    x xn f xn , t n f xn 1 , t n 1 t
    2
    1
    3
    xn 1 xn f xn , t n f xn21 , t n 1 t
    2
    ...
    2
    n 1

    1
    m 1
    x xn f xn , t n f xn 1 , t n 1 t
    2
    m
    m 1
    stop if xn 1 xn 1 threshold
    m
    n 1

    Method of Propagation 3

    Symplectic Integrator: special integrator for


    classical mechanics made to satisfy Hamiltons
    Equation dp
    H
    dq H

    dt
    q
    dt p
    Second order Symplectic assume H=T(p)+V(q)
    V qn
    t
    pn 0.5 pn 0.5 p n t pn 0.5
    q

    T pn 0.5
    qn 1 qn
    t
    p
    V qn 1
    t
    pn 1 pn 0.5 0.5
    q

    Intermolecular Interaction: Super


    Molecule Approximation

    Super Molecule Approximation


    To obtain the interaction between two waters perform
    calculation of two waters

    Two things to be careful


    Size Consistency
    Basis set super position erro

    Size Consistancy

    Consider H2H2 with CISD infinite far away


    result for H2H2 is not equal to 2 H2!!

    Two electron
    excitation

    H2A

    H2A

    H2B

    H2A

    H2B

    Two electron excitation of


    two H2 has four electron
    excitation in H2H2

    Two electron
    excitation

    H2A

    H2B

    H2A

    H2A

    H2B

    Size Consistent Methods


    MP2
    CCSD
    CCSD exp

    T1 T2

    D0

    1
    T1 D0 T2 D0 T1T1 D0 T2T2 D0 T1T2 D0
    2
    Pople et al. have defined an empirical estimation of the four electron
    excitation contribution MRSDCI had defined +Q so for bond dissociation
    and potential energy surface calculation people use MRSDCI+Q to
    approximately take care of the size consistancy problem

    Basis Set Super Position Error


    When calculating the energy of a
    supermolecule we use the basis set of
    Molecule A and Molecule B together, when
    we calculate the separated products we
    calculate molecule A with basis of A, molecule
    B with basis of B

    VS

    Counter Poise Correction


    Boys Lanbardi method: use ghost atoms (no
    charge just position to put basis)and put the
    basis for the respective partner in the energy
    calculation for molecule A and B

    VS

    BSSE big for small basis sets

    Gaussian CP Input

    G09 CP output 1

    G09 CP output2

    G09 CP output3

    G09 CP output4

    G09 CP Output 5

    G09 CP output 6

    Optimized Geometry CP

    W/O CP

    with CP

    Excited Electronic States


    Calculation

    Method for Excited States


    Use more than one slater determinant

    CISD: Configuration Interaction Singles and Doubles


    CCSD: Coupled Cluster Singles and Doubles
    MCSCF: Multiconfigurational Self Consistent Field
    MR-CISD: Multireference CISD

    CAS MP2
    MP2,3,4: Mollar Plesset perturbation theory

    Equation of Motion CCSD


    Time Dependent DFT

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