Molecular dynamics simulation
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Applied Statistical Mechanics Lecture Note - 13. Molecular Dynamics Simulation. 고려대학교 화공생명공학과 강정원. Contents. Basic Molecular Dynamics Simulation Method Properties Calculations in MD MD in Other Ensembles. Basic MD Simulation - MC vs. MD. MC Probabilistic simulation technique

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Molecular Dynamics Simulation

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Molecular dynamics simulation

Applied Statistical Mechanics

Lecture Note - 13

Molecular Dynamics Simulation

고려대학교

화공생명공학과

강정원


Contents

Contents

  • Basic Molecular Dynamics Simulation Method

  • Properties Calculations in MD

  • MD in Other Ensembles


Basic md simulation mc vs md

Basic MD Simulation - MC vs. MD

  • MC

    • Probabilistic simulation technique

    • Limitations

      • require the knowledge of an equilibrium distribution

      • rigorous sampling of large number of possible phase-space

      • gives only configurational properties (not dynamic properties !)

  • MD

    • Deterministic simulation technique

    • Fully numerical formalism

      • numerical solution of N-body system


Basic md simulation the idea

Basic MD Simulation - The Idea

  • Follow the exactly same procedure as real experiments

    • Prepare sample

      • prepare N particles

      • solve equation of motions

    • Connect sample to measuring instruments (e.g. thermometer, viscometer,…)

      • after equilibration time, actual measurement begins

    • Measure the property of interest for a certain time interval

      • average properties

  • Example : measurement of temperature


Basic md simulation equation of motion

Basic MD Simulation - Equation of Motion

  • Classical Newton’s equation of motion

    • Three formulation

      • Newtonian

      • Lagrangian

      • Hamiltonian

    • Hamiltonian preferred for many-body systems

      • solution of 2N differential equations

Solution methods : Finite Difference Method


Basic md simulation verlet algorithm

Basic MD Simulation - Verlet Algorithm

  • Verlet (1967) : Very simple, efficient and popular algorithm

feature : update without calculating momentum (p)


Basic md simulation leapfrog algorithm

Basic MD Simulation - Leapfrog Algorithm

  • Hockeny (1970), Potter (1972)

  • Half-step leap-frog algorithm

  • Mathematically equivalent to Verlet algorithm


2 properties calculation in md energies

2. Properties Calculation in MD- Energies

  • Potential energy

    • Can be calculated during force calculation

  • Kinetic energy


2 properties calculation in md pressures

In an MD simulation, calculation of pressure using tensor notation is not the most efficient method.

For homogeneous systems, there is simple way to calculate pressure (Irving and Kirkwood, 1950)

2. Properties Calculation in MD- Pressures

Configurational – called “Virial”

Kinetic – ideal gas term

Calculate when force update

Calculate when velocity update


2 properties calculation in md transport properties

2. Properties Calculation in MD- Transport Properties

  • Approaches for transport properties

    • Method 1 : NEMD (Non-equilibrium Molecular Dynamics)

      • Continuous addition and removal of conserved quantities

      • Gives high signal-to-noise ratio (good statistics)

    • Method 2 : Equilibrium molecular dynamics

      • Start with anisotropic configuration of mass, momentum and energy

      • Observe natural fluctuations and dissipation of mass, momentum and energy

      • Poor signal-to-noise ration (poor statistics)

      • All transport properties can be measured at once


2 properties calculation in md transport properties1

Differential Balance Equation

Constitutive Equations

2. Properties Calculation in MD- Transport Properties


2 properties calculation in md transport properties2

2. Properties Calculation in MD- Transport Properties

  • Purpose : Obtain transport coefficient by molecular simulation

    • Not that the “laws” are only approximation that apply not-too-large gradients

    • In principle transfer coefficients depends on c, T and v

  • Green-Kubo Relation

    • Relation between transport properties and integral over time-correlation function.


2 properties calculation in md transport properties3

Consider self-diffusion in a pure substance

Consider how molecules are dissipated when initial configurations are given as Dirac delta function

Combine mass balance eqn. With Fick’s Law

2. Properties Calculation in MD- Transport Properties

Dimensionality

of given system

Solution

B.C.


2 properties calculation in md transport properties4

2. Properties Calculation in MD- Transport Properties

We do not need concentration itself c(r,t) - just diffusion coefficient (D)


2 properties calculation in md transport properties5

2. Properties Calculation in MD- Transport Properties

Slope here gives D

  • Plot of t vs. square of traveled distance gives diffusion coefficient

  • In 3D –space, <r2> is mean square displacement (MSD)


2 properties calculation in md transport properties6

An alternative formulation using velocity instead of particle position

2. Properties Calculation in MD- Transport Properties


2 properties calculation in md transport properties7

2. Properties Calculation in MD- Transport Properties

  • Autocorrelation function :

    • property difference between two adjacent time steps

  • Area under the curve gives the value of self-diffusion coefficient


2 properties calculation in md evaluation of time correlation functions

A(t0)

A(t0)

A(t0)

A(t1)

A(t1)

A(t1)

A(t2)

A(t2)

A(t2)

A(t3)

A(t3)

A(t3)

A(t4)

A(t4)

A(t4)

A(t5)

A(t5)

A(t5)

A(t6)

A(t6)

A(t6)

A(t7)

A(t7)

A(t7)

A(t8)

A(t8)

A(t8)

A(t9)

A(t9)

A(t9)

2. Properties Calculation in MD- Evaluation of time correlation functions

  • Time consuming and require a lot of storage

    • Alternative method : FFT (Fast Fourier Transform), Coarse Graining method

+...

A0A1

+

A1A2

+

A2A3

+

A3A4

+

A4A5

+

A5A6

+

A6A7

+

A7A8

+

A8A9

+...

A0A2

+

A1A3

+

A2A4

+

A3A5

+

A4A6

+

A5A7

+

A6A8

+

A7A9

A0A5

+

A1A6

+

A2A7

+

A3A8

+

A4A9

+...


2 properties calculation in md transport properties8

Zero-shear viscosity

Thermal Conductivity

2. Properties Calculation in MD- Transport Properties


2 properties calculation in md radial distribution function

Time averaged value of number density

Ensemble averaged number density

2. Properties Calculation in MD- Radial Distribution Function

1

Just count the number of molecules within a range


3 md in other ensembles constraints

With proper choice of g(r), we can calculate useful thermodynamic properties

Internal energy

Pressure

Chemical Potential

3. MD in Other Ensembles - Constraints


3 md in other ensembles constraints1

3. MD in Other Ensembles – Constraints

  • Hamiltonian formulation

    • Conservation of kinetic + potential energy

      H = K + U

    • (N,V,E) ensemble

    • Cannot be applied to other ensemble

      • constant T, constant P, …

      • for example we can keep const T while H is constant

      • distribution of K and U

  • Two types of constraints

    • Holonomic constraints : may be integrated out of equation of motion

    • Nonholonomic constraints : non-integrable (involves velocities)

      • Temperature, pressure, stress, …


3 md in other ensembles constraints2

3. MD in Other Ensembles – Constraints

  • Force momentum temperature to remain constant

  • One (bad) approach

    • at each time step scale momenta to force K to desired value

      • advance positions and momenta

      • apply pnew = lp with l chosen to satisfy

      • repeat

    • “equations of motion” are irreversible

      • “transition probabilities” cannot satisfy detailed balance

    • does not sample any well-defined ensemble


3 md in other ensembles constraints3

3. MD in Other Ensembles – Constraints

  • “Gauss’ principle of least constraints”

    • Gaussian constraints : perturbative force introduced into the equation of motion minimizes the deviation to classical trajectories of particles from their unperturbed trajectories

    • Consider a function f , a function of particle acceleration

    • f=0 : normal Newtonian equation of motion

    • otherwise, constrained non-Newtonian equation of motion

    • Gauss’ principle : physical acceleration  f to be minimum


3 md in other ensembles constraints4

3. MD in Other Ensembles – Constraints

  • Constant Temperature constraints

Constraint force

Newtonian


3 md in other ensembles constraints5

3. MD in Other Ensembles – Constraints

  • Modified equation of motion

one of good approach, but temperature is not specified !


3 md in other ensembles nose thermostat

3. MD in Other Ensembles – Nose Thermostat

  • Extended Lagrangian Equation of Motion


3 md in other ensembles nose hoover thermostat

t-dt t t+dt

r

v

F

3. MD in Other Ensembles – Nose-Hoover Thermostat

  • Equations of motion

  • Integration schemes

    • predictor-corrector algorithm is straightforward

    • Verlet algorithm is feasible, but tricky to implement

At this step, update of x depends on p; update of p depends on x


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