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## Flow Chart For a Typical MD Program

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**SMA5233 Particle Methods and Molecular DynamicsLecture 6:**Coarse-grained hybrid MDA/P Chen Yu ZongTel: 6516-6877Email: phacyz@nus.edu.sghttp://bidd.nus.edu.sgRoom 08-14, level 8, S16 National University of Singapore**Flow Chart For a Typical MD Program**Initialize Variables Build Model Define Material Set Boundary Conditions Start Initialize Variables • Define the positions of the atoms • Assign randomly generated velocities Integrate End**Flow Chart For a Typical MD Program**Initialize Variables Build Model Define Material Set Boundary Conditions Start Build Model • Define the simulation domain • Build atoms to lattice Integrate End**Flow Chart For a Typical MD Program**Initialize Variables Build Model Define Material Set Boundary Conditions Start Define Material • Specify interatomic potentials Integrate End**Flow Chart For a Typical MD Program**Initialize Variables Build Model Define Material Set Boundary Conditions Start Set Boundary Conditions • Set initial temperature distribution • Specify thermodynamic controls Integrate End**Flow Chart For a Typical MD Program**Initialize Variables Build Model Define Material Set Boundary Conditions Start Start • Compute the forces at time=0 • Set frequency of outputs Integrate End**Flow Chart For a Typical MD Program**Initialize Variables Build Model Define Material Set Boundary Conditions Start Integrate • Compute the atomic trajectories • Compute other desired outputs Integrate End**Flow Chart For a Typical MD Program**Initialize Variables Build Model Define Material Set Boundary Conditions Start End • Compute final thermodynamic outputs • Calculate program statistics Integrate End**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 Fully Atomistic Simulations Limitations**Coarse-grained Model**• DNA Sugar and Phosphate groups reduced to one molecule(bead) • Each DNA base is represented by one molecule(bead) Coarse-grained Model Fully Atomistic Model**Computationally less expensive**Decreases degrees of freedom Advantages of the Coarse-grained Model • Allows for longer DNA duplexes • Time length up to microsecond Coarse-grained model DNA duplex Chemical structure of DNA duplex**Coarse-grained Model**• One or multiple amino acids reduced to one molecule(bead)**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