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SMA5233 Particle Methods and Molecular Dynamics Lecture 6: Coarse-grained hybrid MD A/P Chen Yu Zong Tel: 6516-6877 Email: [email protected] http://bidd.nus.edu.sg Room 08-14, level 8, S16 National University of Singapore. Flow Chart For a Typical MD Program. Initialize Variables. Build - PowerPoint PPT Presentation
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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: [email protected]@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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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
