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    Intro 2 MD Simulation

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    achsanuddin
    Molecular dynamics simulations describe the motions of nuclei in a molecule classically using Newton's equations of motion. The potential energy is approximated empirically using a force field that accounts for bonded and non-bonded interactions. The equations of motion are integrated numerically using algorithms like leapfrog integration with time steps around 1 femtosecond. While molecular dynamics simulations provide atomic-level insight, they are computationally expensive and can currently only simulate small systems over short timescales.

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    Intro 2 MD Simulation

    Uploaded by

    achsanuddin
    228 views20 pages
    Molecular dynamics simulations describe the motions of nuclei in a molecule classically using Newton's equations of motion. The potential energy is approximated empirically using a force field that accounts for bonded and non-bonded interactions. The equations of motion are integrated numerically using algorithms like leapfrog integration with time steps around 1 femtosecond. While molecular dynamics simulations provide atomic-level insight, they are computationally expensive and can currently only simulate small systems over short timescales.

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    Molecular dynamics simulations describe the motions of nuclei in a molecule classically using Newton's equations of motion. The potential energy is approximated empirically using a force field that accounts for bonded and non-bonded interactions. The equations of motion are integrated numerically using algorithms like leapfrog integration with time steps around 1 femtosecond. While molecular dynamics simulations provide atomic-level insight, they are computationally expensive and can currently only simulate small systems over short timescales.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    228 views20 pages

    Intro 2 MD Simulation

    Uploaded by

    achsanuddin
    Molecular dynamics simulations describe the motions of nuclei in a molecule classically using Newton's equations of motion. The potential energy is approximated empirically using a force field that accounts for bonded and non-bonded interactions. The equations of motion are integrated numerically using algorithms like leapfrog integration with time steps around 1 femtosecond. While molecular dynamics simulations provide atomic-level insight, they are computationally expensive and can currently only simulate small systems over short timescales.

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    Molecular Dynamics simulations

    Bert de Groot
    Max Planck institute for biophysical chemistry
    Göttingen, Germany
    Molecular Dynamics Simulations

    Schrödinger equation

    Born-Oppenheimer approximation

    Nucleic motion described classically

    Empirical force field


    Molecular Dynamics Simulations

    Interatomic interactions
    Molecular dynamics-(MD) simulations of Biopolymers
    d2
    • Motions of nuclei are described classically, ( ∗ ) ma 2 Rα = −∇α Eel ( R1 ,..., RN ), α = 1,..., N .
    dt
    • Potential function Eel describes the electronic influence on motions of the nuclei and is
    approximated empirically  „classical MD“:

    E el ≈ ∑
    Bindungen
    E ibond + ∑E
    Bindungs −
    angle
    j + ∑E
    Dihedral −
    dihe
    k + ∑ ( EαCoul
    ,β + Eα ,β + Eα ,β ) + ...,
    . rep . vdW

    i winkel j winkel k

    Covalent bonds Non-bonded interactions

    Eibond
    approximated

    exact
    =
    KBT { R=
    ν0 |R|
    „Force-
    Field“
    Molecular Dynamics Simulation
    Molecule: (classical) N-particle system

    d2  
    Newtonian equations of motion: mi 2 ri = Fi ( r )
    dt

    Fi (r ) = −∇ iV (r )
     
    with r = ( r1 ,..., rN )
    Integrate numerically via the „leapfrog“ scheme:

    with
    Δt ≈ 1fs!

    (equivalent to the Verlet algorithm)


    BPTI: Molecular Dynamics (300K)
    Computational task:
    Solve the Newtonian equations of motion:
    Non-bonded interactions

    Lennard-Jones potential Coulomb potential


    Use of constraints to
    increase the integration step

    The „SHAKE“ algorithm


    Δt = 1fs --> 2 fs
    Molecular dynamics is very expensive ...
    Example: F1-ATPase in water (183 674 atoms), 1 nanosecond:
    106 integration steps
    8.4 * 1011 flop per step [n(n-1)/2 interactions]

    total: 8.4 * 1017 flop


    on a 100 Mflop/s workstation: ca 250 years

    ...but performance has been improved by use of:


    multiple time stepping ca. 25 years
    + structure adapted multipole methods ca. 6 years
    + FAMUSAMM ca. 2 years
    + parallel computers ca. 55 days
    Limits of MD-Simulations

    • classical description:

    chemical reactions not described


    poor description of H-atoms (proton-transfer)
    poor description of low-T (quantum) effects
    simplified electrostatic model
    simplified force field

    • only small systems accessible (104 ... 106 atoms)

    • only short time spans accessible (ps ... μs)


    MD-Experiments with Argon Gas
    Role of environment - solvent
    explicit
    or
    implicit?

    box
    or
    droplet?
    Surface (tension) effects?
    periodic boundary conditions
    and the minimum image convention
    Proteins jump between many, hierarchically ordered
    „conformational substates“

    H. Frauenfelder et al., Science 229 (1985) 337


    Reversible Folding Dynamics of a β-Peptide

    X. Daura, B. Jaun, D. Seebach, W.F. van Gunsteren, A.E. Mark, J. Mol. Biol. 280 (1998) 925
    MD Simulations

    • external coupling:

    temperature (potential truncation, integration errors)


    pressure (density equilibration)
    system translation/rotation

    • analysis

    energies (individual terms, pressure, temperature)


    coordinates (numerical analysis, visual inspection!)
     mechanisms

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