Presentation is loading. Please wait.

Presentation is loading. Please wait.

SMA5233 Particle Methods and Molecular Dynamics Lecture 6: Coarse-grained hybrid MD A/P Chen Yu Zong Tel: 6516-6877

Similar presentations


Presentation on theme: "SMA5233 Particle Methods and Molecular Dynamics Lecture 6: Coarse-grained hybrid MD A/P Chen Yu Zong Tel: 6516-6877"— Presentation transcript:

1 SMA5233 Particle Methods and Molecular Dynamics Lecture 6: Coarse-grained hybrid MD A/P Chen Yu Zong Tel: 6516-6877 Email: phacyz@nus.edu.sg http://bidd.nus.edu.sg Room 08-14, level 8, S16 National University of Singapore phacyz@nus.edu.sg http://bidd.nus.edu.sgphacyz@nus.edu.sg http://bidd.nus.edu.sg

2 2 Flow Chart For a Typical MD Program Initialize Variables Build Model Define Material Start Integrate Set Boundary Conditions End Define the positions of the atoms Assign randomly generated velocities Initialize Variables

3 3 Flow Chart For a Typical MD Program Initialize Variables Build Model Define Material Start Integrate Set Boundary Conditions End Define the simulation domain Build atoms to lattice Build Model

4 4 Flow Chart For a Typical MD Program Initialize Variables Build Model Define Material Start Integrate Set Boundary Conditions End Specify interatomic potentials Define Material

5 5 Flow Chart For a Typical MD Program Initialize Variables Build Model Define Material Start Integrate Set Boundary Conditions End Set initial temperature distribution Specify thermodynamic controls Set Boundary Conditions

6 6 Flow Chart For a Typical MD Program Initialize Variables Build Model Define Material Start Integrate Set Boundary Conditions End Compute the forces at time=0 Set frequency of outputs Start

7 7 Flow Chart For a Typical MD Program Initialize Variables Build Model Define Material Start Integrate Set Boundary Conditions End Compute the atomic trajectories Compute other desired outputs Integrate

8 8 Flow Chart For a Typical MD Program Initialize Variables Build Model Define Material Start Integrate Set Boundary Conditions End Compute final thermodynamic outputs Calculate program statistics End

9 9 Fully Atomistic Simulations Computation of material properties based on explicit treatment of atomic degrees of freedom Computationally expensive Too many degrees of freedom Only capable on small DNA duplexes Time duration in nanoseconds Limitations

10 10 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

11 11 Advantages of the Coarse-grained Model Computationally less expensive Decreases degrees of freedom Coarse-grained model DNA duplex  Allows for longer DNA duplexes  Time length up to microsecond Chemical structure of DNA duplex

12 12 Coarse-grained Model One or multiple amino acids reduced to one molecule(bead)

13 Intra-Polymer Forces – Combinations Of the Following: Stiff (Fraenkel) / Hookean Spring Lennard-Jones Repulsion Finitely-Extensible Non-linear Elastic (FENE) Spring

14 Intra-Polymer Forces – Combinations Of the Following: Lennard-Jones Repulsion Finitely-Extensible Non-linear Elastic (FENE) Spring

15 Intra-Polymer Forces (continued) Stiff: Schlijper, Hoogerbrugge, Manke, 1995 Hookean + Lennard-Jones: Nikunen, Karttunen, Vattulainen, 2003 FENE: Chen, Phan-Thien, Fan, Khoo, 2004 Marko-Siggia WormLike Chain Can be adjusted if M>2 (Underhill, Doyle 2004)

16 16 An Example

17 17 An Example

18 18 An Example

19 19 An Example

20 20 An Example

21 21 An Example

22 22 An Example

23 23 An Example

24 24 An Example

25 25 A Case Study

26 26 A Case Study

27 27 A Case Study

28 28 A Case Study


Download ppt "SMA5233 Particle Methods and Molecular Dynamics Lecture 6: Coarse-grained hybrid MD A/P Chen Yu Zong Tel: 6516-6877"

Similar presentations


Ads by Google