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Molecular Simulation

Molecular Simulation. 黃鎮剛 交通大學 生物科技系及生物資訊所. Empirical Force Field. http://life.nctu.edu.tw/~jkhwang/molsim. Free software. VMD & NAMD Molecular Dynamics, Graphics (OpenGL) SwissPDB Viewer Minimization, Modeling, Graphics (OpenGL) Cn3D Strutcure alignment, Graphics (OpenGL) Rasmol

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Molecular Simulation

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  1. Molecular Simulation 黃鎮剛 交通大學 生物科技系及生物資訊所

  2. Empirical Force Field • http://life.nctu.edu.tw/~jkhwang/molsim

  3. Free software • VMD & NAMD • Molecular Dynamics, Graphics (OpenGL) • SwissPDB Viewer • Minimization, Modeling, Graphics (OpenGL) • Cn3D • Strutcure alignment, Graphics (OpenGL) • Rasmol • Graphics (2D)

  4. Warming up • Let's take a look at VMD

  5. Molecular Simulation Jump Start • Quick Start

  6. A simple empirical force field

  7. Analysis of molecular topology • Bonded interactions • The number of bonds • 1-2 interactions • The number of angles • 1-3 interactions • The number of torsions • 1-4 interactions • Non-bonded interactions • Van der Waals and electrostatic interactions • The nunmber of nonbonded interactions

  8. ?? bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  9. How many types of bonds? ?? bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  10. How many types of bonds? C-C C-H ?? bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  11. How many types of bonds? C-C 2 C-H 8 ?? bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  12. How many types of bonds? C-C 2 C-H 8 10 bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  13. How many types of angles? 10 bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  14. How many types of angles? C-C-C C-C-H H-C-H 10 bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  15. How many types of angles? C-C-C 1 C-C-H 10 H-C-H 7 10 bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

  16. How many types of angles? C-C-C 1 C-C-H 10 H-C-H 7 10 bonds 18 angle terms ?? torsional terms ?? non-bonded interactions

  17. How many types of torsions? 10 bonds 18 angle terms ?? torsional terms ?? non-bonded interactions

  18. How many types of torsions? H-C-C-H H-C-C-C 10 bonds 18 angle terms ?? torsional terms ?? non-bonded interactions

  19. How many types of torsions? H-C-C-H 12 H-C-C-C 6 10 bonds 18 angle terms 18 torsional terms ?? non-bonded interactions

  20. How many types of nonbonded ineractions? 10 bonds 18 angle terms 18 torsional terms ?? non-bonded interactions

  21. How many types of nonbonded ineractions? H-H C-C 10 bonds 18 angle terms 18 torsional terms ?? non-bonded interactions

  22. How many types of nonbonded ineractions? H-H 21 C-C 6 10 bonds 18 angle terms 18 torsional terms 27 non-bonded interactions

  23. Force field parameters • Transferability • A C-H is a C-H, no matter where it occurs. • Force fields are empirical, there is no so-called "correct" form for a force field. • The form of force field is a compromise between "accuracy" and "computational efficiency".

  24. Atom types • Contains information about hybridization and sometimes the local environment. • sp3, sp2, sp • The reference angles is 109.5 for sp3 carbon and 110 for sp2 carbon

  25. Bond stretching • Morse potential • Harmonic potential

  26. K in kcal/mol/A2 C_04 H_01 250.0 1.090 C_04 C_04 250.0 1.523 C_04 C_03 250.0 1.534 C_04 N_03 250.0 1.470 C_04 N_04 200.0 1.430 C_04 O_01 200.0 1.430 C_03 C_03 500.0 1.393 C_03 H_01 50.00 1.024 C_03 N_03 500.0 1.324 C_03 N_04 500.0 1.339 C_03 O_00 500.0 1.235 C_03 O_01 500.0 1.460 C_04 S_02 250.0 1.789 N_03 H_01 250.0 1.040 N_04 H_01 250.0 1.039 O_01 H_01 252.0 0.970 S_02 H_01 250.0 1.000

  27. K in kcal/mol/A2 C_04 H_01 250.0 1.090 C_04 C_04 250.0 1.523 C_04 C_03 250.0 1.534 C_04 N_03 250.0 1.470 C_04 N_04 200.0 1.430 C_04 O_01 200.0 1.430 C_03 C_03 500.0 1.393 C_03 H_01 50.00 1.024 C_03 N_03 500.0 1.324 C_03 N_04 500.0 1.339 C_03 O_00 500.0 1.235 C_03 O_01 500.0 1.460 C_04 S_02 250.0 1.789 N_03 H_01 250.0 1.040 N_04 H_01 250.0 1.039 O_01 H_01 252.0 0.970 S_02 H_01 250.0 1.000

  28. K in kcal/mol C_03 C_03 C_04 120.0 120.0 C_03 C_03 C_03 120.0 119.9 C_03 C_03 H_01 60.0 120.0 C_03 N_04 C_04 60.0 124.0 C_03 N_04 H_01 60.0 120.0 C_04 N_04 H_01 60.0 109.9 H_01 N_04 H_01 60.0 120.0 H_01 N_03 H_01 60.0 113.9 C_04 N_03 C_04 60.0 110.6 C_04 N_03 H_01 60.0 113.0 C_03 N_03 C_04 60.0 120.9 C_03 N_03 H_01 60.0 120.4 Lp__ N_03 Lp__ 50.0 130.0 Lp__ N_03 H_01 50.0 109.0 Lp__ N_03 C_04 50.0 109.0 C_03 O_01 H_01 60.0 120.0 C_03 O_01 H_01 40.0 120.0 C_04 O_01 H_01 60.0 120.9 C_04 O_01 C_04 50.0 119.0 H_01 O_01 H_01 50.0 110.0 Lp__ O_01 Lp__ 50.0 130.0 Lp__ O_01 H_01 50.0 109.0 Lp__ O_01 C_04 50.0 109.0 Lp__ O_01 C_03 50.0 120.0 H_01 C_04 H_01 60.0 109.2 H_01 C_04 O_01 60.0 109.2 C_04 C_04 C_04 60.0 111.1 C_04 C_04 H_01 60.0 109.2 C_04 C_04 N_03 60.0 108.2 C_04 C_04 O_01 60.0 109.8 C_03 C_04 C_04 60.0 109.8 C_03 C_04 H_01 60.0 109.2 C_03 C_04 N_03 60.0 112.3 C_03 C_04 O_01 60.0 110.0 N_04 C_04 C_04 60.0 110.9 N_04 C_04 H_01 60.0 109.2 N_03 C_04 H_01 60.0 108.2 N_03 C_04 N_03 120.0 120.0 H_01 C_03 H_01 40.0 120.0 N_03 C_03 O_00 120.0 123.1 N_04 C_03 N_04 120.0 119.9 O_00 C_03 H_01 120.0 119.9 O_01 C_03 O_00 120.0 122.3 C_04 C_03 H_01 60.0 119.2 C_04 C_03 N_03 60.0 117.5 C_04 C_03 O_00 60.0 119.2 C_04 C_03 O_01 60.0 119.2

  29. C_04 C_04 1.40 3 0.0 C_04 C_03 0.00 2 180.0 C_04 O_01 0.60 3 0.0 C_03 C_03 10.00 2 180.0 C_03 C_00 10.00 2 180.0 C_03 H_01 10.00 2 180.0 C_03 N_03 7.50 2 180.0 C_03 O_00 0.00 1 0.0 C_03 O_01 0.00 1 0.0 H_01 N_03 7.50 2 180.0 N_03 C_04 0.00 3 0.0 N_04 C_04 1.40 3 0.0 N_04 C_03 10.00 2 180.0 N_04 H_01 7.50 2 180.0 S_02 C_04 1.00 3 0.0 S_02 C_03 0.00 3 0.0 S_02 S_02 6.00 2 0.0

  30. The parameters depend only on 2,3 atoms C_04 C_04 1.40 3 0.0 C_04 C_03 0.00 2 180.0 C_04 O_01 0.60 3 0.0 C_03 C_03 10.00 2 180.0 C_03 C_00 10.00 2 180.0 C_03 H_01 10.00 2 180.0 C_03 N_03 7.50 2 180.0 C_03 O_00 0.00 1 0.0 C_03 O_01 0.00 1 0.0 H_01 N_03 7.50 2 180.0 N_03 C_04 0.00 3 0.0 N_04 C_04 1.40 3 0.0 N_04 C_03 10.00 2 180.0 N_04 H_01 7.50 2 180.0 S_02 C_04 1.00 3 0.0 S_02 C_03 0.00 3 0.0 S_02 S_02 6.00 2 0.0

  31. Improper torsional angles

  32. Improper torsional angles 1 2 3 4

  33. Improper torsional angles 1 2 3 4

  34. Atom ro e C_03 1.75 3.9202 0.0376 C_04 1.85 3.9150 0.0738 H_01 1.10 2.6525 0.0010 N_03 1.65 3.2171 0.4132 O_00 1.60 3.2005 0.1848 O_01 1.60 3.2005 0.1848 S_02 1.85 3.9150 0.0738 Lp__ 1.10 2.6525 0.0010

  35. Cross-term interactions

  36. Cross terms • Stretch-stretch • Stretch-torsion • Stretch-bend • Bend-torsion • Bend-bend • These terms are important for vibrational frequency prediction.

  37. Staggering effect

  38. Staggering effect Carbon: +1 Lone electron -1/2

  39. Polarization

  40. Polarization Approximation Electrostatic field does not include contributions from atom i

  41. Polarization H H O New model

  42. Polarization is computational intensive • Its effects is important in the simulation of ionic solution. The system usually contains atom or ions and small molecules.

  43. Solvent dielectric models Effetive dielectric constant

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