Transcript Coarse-grained hybrid MD - BIDD - National University of Singapore

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
Model
Define
Material
Initialize Variables
Set
Boundary
Conditions
Start
•Define the positions of the atoms
•Assign randomly generated velocities
Integrate
End
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Flow Chart For a Typical MD Program
Initialize
Variables
Build
Model
Build Model
Define
Material
Set
Boundary
Conditions
Start
•Define the simulation domain
•Build atoms to lattice
Integrate
End
3
Flow Chart For a Typical MD Program
Initialize
Variables
Build
Model
Define Material
Define
Material
Set
Boundary
Conditions
Start
•Specify interatomic potentials
Integrate
End
4
Flow Chart For a Typical MD Program
Initialize
Variables
Build
Model
Set Boundary Conditions
Define
Material
Set
Boundary
Conditions
Start
•Set initial temperature distribution
•Specify thermodynamic controls
Integrate
End
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Flow Chart For a Typical MD Program
Initialize
Variables
Build
Model
Start
Define
Material
Set
Boundary
Conditions
Start
•Compute the forces at time=0
•Set frequency of outputs
Integrate
End
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Flow Chart For a Typical MD Program
Initialize
Variables
Build
Model
Integrate
Define
Material
Set
Boundary
Conditions
Start
•Compute the atomic trajectories
•Compute other desired outputs
Integrate
End
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Flow Chart For a Typical MD Program
Initialize
Variables
Build
Model
Define
Material
End
Set
Boundary
Conditions
Start
•Compute final thermodynamic outputs
•Calculate program statistics
Integrate
End
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Fully Atomistic Simulations
Computation of material
properties based on
explicit treatment of
atomic degrees of
freedom
Limitations
Computationally
expensive
Too many degrees of
freedom
Only capable on small
DNA duplexes
Time duration in
nanoseconds
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Coarse-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 Model
Computationally less expensive
Allows for longer DNA duplexes
Decreases degrees of freedom
Time length up to microsecond
Coarse-grained model DNA duplex
Chemical structure of DNA duplex
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Coarse-grained Model
•One or multiple amino acids reduced to one molecule(bead)
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Intra-Polymer Forces – Combinations Of the Following:
• Lennard-Jones Repulsion
• Stiff (Fraenkel) / Hookean Spring
• 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)
• Marko-Siggia WormLike Chain
Can be adjusted if M>2
(Underhill, Doyle 2004)
Stiff: Schlijper, Hoogerbrugge, Manke, 1995
Hookean + Lennard-Jones: Nikunen, Karttunen, Vattulainen, 2003
FENE: Chen, Phan-Thien, Fan, Khoo, 2004
An Example
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An Example
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An Example
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An Example
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An Example
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An Example
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An Example
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An Example
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A Case Study
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A Case Study
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A Case Study
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A Case Study
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