SMA5233 SMA5233 Particle Methods and Molecular DynamicsParticle Methods and Molecular Dynamics

Lecture 6: Coarse-grained hybrid MDLecture 6: Coarse-grained hybrid MD

A/P Chen Yu ZongA/P Chen Yu Zong

Tel: 6516-6877Tel: 6516-6877Email: Email: phacyz@nus.edu.sgphacyz@nus.edu.sg

http://http://bidd.nus.edu.sgbidd.nus.edu.sgRoom 08-14, level 8, S16 Room 08-14, level 8, S16

National University of SingaporeNational University of Singapore

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Flow Chart For a Typical MD ProgramFlow Chart For a Typical MD Program

InitializeVariables

BuildModel

DefineMaterial

Start

Integrate

SetBoundary Conditions

End

•Define the positions of the atoms

•Assign randomly generated velocities

Initialize Variables

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Flow Chart For a Typical MD ProgramFlow Chart For a Typical MD Program

InitializeVariables

BuildModel

DefineMaterial

Start

Integrate

SetBoundary Conditions

End

•Define the simulation domain

•Build atoms to lattice

Build Model

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Flow Chart For a Typical MD ProgramFlow Chart For a Typical MD Program

InitializeVariables

BuildModel

DefineMaterial

Start

Integrate

SetBoundary Conditions

End

•Specify interatomic potentials

Define Material

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Flow Chart For a Typical MD ProgramFlow Chart For a Typical MD Program

InitializeVariables

BuildModel

DefineMaterial

Start

Integrate

SetBoundary Conditions

End

•Set initial temperature distribution

•Specify thermodynamic controls

Set Boundary Conditions

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Flow Chart For a Typical MD ProgramFlow Chart For a Typical MD Program

InitializeVariables

BuildModel

DefineMaterial

Start

Integrate

SetBoundary Conditions

End

•Compute the forces at time=0

•Set frequency of outputs

Start

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Flow Chart For a Typical MD ProgramFlow Chart For a Typical MD Program

InitializeVariables

BuildModel

DefineMaterial

Start

Integrate

SetBoundary Conditions

End

•Compute the atomic trajectories

•Compute other desired outputs

Integrate

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Flow Chart For a Typical MD ProgramFlow Chart For a Typical MD Program

InitializeVariables

BuildModel

DefineMaterial

Start

Integrate

SetBoundary Conditions

End

•Compute final thermodynamic outputs

•Calculate program statistics

End

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Fully Atomistic SimulationsFully Atomistic Simulations

Computation of material Computation of material properties based on properties based on explicit treatment of explicit treatment of atomic degrees of atomic degrees of freedomfreedom

Computationally Computationally expensiveexpensive

Too many degrees of Too many degrees of freedomfreedom

Only capable on small Only capable on small DNA duplexesDNA duplexes

Time duration in Time duration in nanosecondsnanoseconds

Limitations

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Coarse-grained ModelCoarse-grained Model

•DNA Sugar and Phosphate groups reduced to one molecule(bead)

•Each DNA base is represented by one molecule(bead)

Fully Atomistic Model Coarse-grained Model

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Advantages of the Coarse-grained ModelAdvantages of the Coarse-grained Model

Computationally less expensiveComputationally less expensive

Decreases degrees of freedomDecreases degrees of freedom

Coarse-grained model DNA duplex

Allows for longer DNA duplexes

Time length up to microsecond

Chemical structure of DNA duplex

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Coarse-grained ModelCoarse-grained Model

•One or multiple amino acids reduced to one molecule(bead)

Intra-Polymer Forces – Combinations Of the Following:

• Stiff (Fraenkel) / Hookean Spring

• Lennard-Jones Repulsion

• Finitely-Extensible Non-linear Elastic (FENE) Spring

Intra-Polymer Forces – Combinations Of the Following:

• Lennard-Jones Repulsion

• Finitely-Extensible Non-linear Elastic (FENE) Spring

Intra-Polymer Forces (continued)

Stiff: Schlijper, Hoogerbrugge, Manke, 1995Hookean + Lennard-Jones: Nikunen, Karttunen, Vattulainen, 2003FENE: Chen, Phan-Thien, Fan, Khoo, 2004

• Marko-Siggia WormLike Chain

Can be adjusted if M>2(Underhill, Doyle 2004)

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An Example An Example

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An Example An Example

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An Example An Example

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An Example An Example

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An Example An Example

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A Case Study A Case Study

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A Case Study A Case Study

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A Case Study A Case Study

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A Case Study A Case Study