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  • Martini L1 Introduction

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    phdcao
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    This document provides an overview of a short course on molecular dynamics (MD) simulation taught by Professor A. Martini. The course objectives are to understand the opportunities and limitations of MD, the tradeoff between model complexity and computational expense, and how to interpret MD studies. The high-level course outline covers the basic concepts of MD including potential energy functions, integration algorithms, boundary conditions, and how to extract static and dynamic properties from simulations. The document provides an introduction to key MD concepts like phase space, ensembles, and references further reading materials.

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    This document provides an overview of a short course on molecular dynamics (MD) simulation taught by Professor A. Martini. The course objectives are to understand the opportunities and limitations of MD, the tradeoff between model complexity and computational expense, and how to interpret MD studies. The high-level course outline covers the basic concepts of MD including potential energy functions, integration algorithms, boundary conditions, and how to extract static and dynamic properties from simulations. The document provides an introduction to key MD concepts like phase space, ensembles, and references further reading materials.

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    Attribution Non-Commercial (BY-NC)
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    223 tayangan12 halaman

    Martini L1 Introduction

    Diunggah oleh

    phdcao
    This document provides an overview of a short course on molecular dynamics (MD) simulation taught by Professor A. Martini. The course objectives are to understand the opportunities and limitations of MD, the tradeoff between model complexity and computational expense, and how to interpret MD studies. The high-level course outline covers the basic concepts of MD including potential energy functions, integration algorithms, boundary conditions, and how to extract static and dynamic properties from simulations. The document provides an introduction to key MD concepts like phase space, ensembles, and references further reading materials.

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    Attribution Non-Commercial (BY-NC)
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    dari 12

    Short Course on Molecular

    Dynamics Simulation

    Lecture 1:
    Basic Concepts

    Professor A. Martini
    Purdue University
    Course Objectives

    ‰ Awareness of the opportunities and limitations


    of MD simulation for scientific and engineering
    research
    ‰ Understanding of the compromise between
    model complexity/realism and computational
    expense
    ‰ Background that enables interpretation of MD
    studies reported in the literature
    ‰ Physical understanding of the theoretic basis of
    MD modeling

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    High Level Course Outline
    1. MD Basics
    2. Potential Energy Functions
    3. Integration Algorithms
    4. Temperature Control
    5. Boundary Conditions
    6. Neighbor Lists
    7. Initialization and Equilibrium
    8. Extracting Static Properties
    9. Extracting Dynamic Properties
    10. Non-Equilibrium MD

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    MD Basics

    ‰ Molecular dynamics (MD) simulation = computational


    tool used to describe how positions, velocities, and
    orientations of molecules change over time.
    ‰ The simulation is based on a set of models that describe
    molecular-scale interactions.
    ‰ These models relate energy/force to configuration which
    are be used to calculate acceleration via Newton’s law.
    ‰ Numerical integration yields particle velocities, and then
    each particle is moved through a distance equal to its
    calculated velocity multiplied by the simulation time step.
    ‰ So, MD is used as a computational “experiment” where a
    system is defined, allowed to evolve, and then
    observations made based on its evolution.

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    MD Basics
    ‰ Experiment ‰ MD Simulation

    Prepare Sample System of particles

    Connect Sample
    to Measuring Solve equations of motion
    Instrument

    Measure Property
    of Interest for Set Extract position and velocity data
    Time Interval

    Average to
    Minimize Use statistical mechanics to extract properties
    Statistical Noise

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    MD Basics
    ‰ Process summary
    Calculate
    Acceleration of
    Each Atom
    Interaction
    Model
    Calculate Total Calculate
    Force on N Velocity of
    Atoms Each Atom
    Initial
    Positions

    Move All Atoms


    to New
    Positions

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    MD Basics
    ‰ Force Æ Acceleration Æ Velocity Æ Position
    v v v
    v v dvi v dri
    vi =
    Fi = mi ai ai =
    dt dt

    i@t+1
    i@t

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    Phase-Space and Ensembles

    ‰ MD conserves the total energy (Hamiltonian)


    N v2
    v v v
    + U (ri )
    pi
    H ( pi , ri ) = ∑
    dH
    =0
    i =1 2mi dt

    PE
    KE

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    Phase-Space and Ensembles

    ‰ A given atom is represented by its time-dependent


    position and momentum vectors

    v v v
    z ri pi = mvi
    i
    y x

    ‰ At a given instant, consider a plot of the positions and


    momenta of all N atoms in the system

    6 N-dimensional plotting domain Æ Phase-Space

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    Phase-Space and Ensembles

    Many Microscopic Systems


    (Statistical Ensembles)

    Macroscopic System

    Property of System = Average Property in all Systems


    ( Ensemble Average)

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    Phase-Space and Ensembles
    ‰ Ensembles characterized by fixed values of
    thermodynamic variables:
    – Energy
    – Temperature
    – Pressure
    – Volume
    – Number of particles
    – Chemical potential
    ‰ Basic MD – NVE
    • Micro-canonical ensemble
    ‰ Other common ensembles – NVT, NPT, μVT
    • Canonical, isothermal-isobaric, grand-canonical

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009


    References
    ‰ The following text books were used throughout
    the development of this course and should be
    used as references for in depth study
    – Allen, M.P and Tildesley, D.J., Computer Simulation
    of Liquids, Oxford University Press.
    – Frenkel, D. and Smit, B., Understanding Molecular
    Simulation: From Algorithms to Applications,
    Elsevier.
    – Haile, J.M., Molecular Dynamics Simulation:
    Elementary Methods, Wiley & Sons.
    – Leach, A., Molecular Modeling: Principles and
    Applications, Prentice Hall.

    Molecular Dynamics Simulation A. Martini Last Updated 8/2009

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