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

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

5 Warming up Let's take a look at VMD

6 Molecular Simulation Jump Start Quick Start

7 A simple empirical force field

8 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

9 ?? bonds ?? angle terms ?? torsional terms ?? non-bonded interactions

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

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

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

13 10 bonds ?? angle terms ?? torsional terms ?? non-bonded interactions How many types of bonds? C-C 2 C-H 8

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

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

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

17 10 bonds 18 angle terms ?? torsional terms ?? non-bonded interactions C-C-C 1 C-C-H 10 H-C-H 7 How many types of angles?

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

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

20 10 bonds 18 angle terms 18 torsional terms ?? non-bonded interactions How many types of torsions? H-C-C-H 12 H-C-C-C 6

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

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

23 10 bonds 18 angle terms 18 torsional terms 27 non-bonded interactions How many types of nonbonded ineractions? H-H 21 C-C 6

24 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".

25 Atom types  Contains information about hybridization and sometimes the local environment.  sp 3, sp 2, sp  The reference angles is for sp 3 carbon and 110 for sp 2 carbon

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28 Bond stretching Morse potential Harmonic potential

29 C_04H_ C_04C_ C_04C_ C_04N_ C_04N_ C_04O_ C_03C_ C_03H_ C_03N_ C_03 N_ C_03O_ C_03O_ C_04 S_ N_03 H_ N_04 H_ O_01 H_ S_02 H_ K in kcal/mol/A 2

30 C_04H_ C_04C_ C_04C_ C_04N_ C_04N_ C_04O_ C_03C_ C_03H_ C_03N_ C_03 N_ C_03O_ C_03O_ C_04 S_ N_03 H_ N_04 H_ O_01 H_ S_02 H_ K in kcal/mol/A 2

31 H_01 C_04 H_ H_01 C_04 O_ C_04 C_04 C_ C_04 C_04 H_ C_04 C_04 N_ C_04 C_04 O_ C_03 C_04 C_ C_03 C_04 H_ C_03 C_04 N_ C_03 C_04 O_ N_04 C_04 C_ N_04 C_04 H_ N_03 C_04 H_ N_03 C_04 N_ H_01 C_03 H_ N_03 C_03 O_ N_04 C_03 N_ O_00 C_03 H_ O_01 C_03 O_ C_04 C_03 H_ C_04 C_03 N_ C_04 C_03 O_ C_04 C_03 O_ K in kcal/mol C_03 C_03 C_ C_03 C_03 C_ C_03 C_03 H_ C_03 N_04 C_ C_03 N_04 H_ C_04 N_04 H_ H_01 N_04 H_ H_01 N_03 H_ C_04 N_03 C_ C_04 N_03 H_ C_03 N_03 C_ C_03 N_03 H_ Lp__ N_03 Lp__ Lp__ N_03 H_ Lp__ N_03 C_ C_03 O_01 H_ C_03 O_01 H_ C_04 O_01 H_ C_04 O_01 C_ H_01 O_01 H_ Lp__ O_01 Lp__ Lp__ O_01 H_ Lp__ O_01 C_ Lp__ O_01 C_

32 C_04C_ C_04C_ C_04O_ C_03 C_ C_03 C_ C_03 H_ C_03 N_ C_03 O_ C_03 O_ H_01N_ N_03 C_ N_04 C_ N_04 C_ N_04 H_ S_02 C_ S_02 C_ S_02 S_

33 C_04C_ C_04C_ C_04O_ C_03 C_ C_03 C_ C_03 H_ C_03 N_ C_03 O_ C_03 O_ H_01N_ N_03 C_ N_04 C_ N_04 C_ N_04 H_ S_02 C_ S_02 C_ S_02 S_ The parameters depend only on 2,3 atoms

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38 Improper torsional angles

39 Improper torsional angles

40 Improper torsional angles

41 Atom r o  C_ C_ H_ N_ O_ O_ S_ Lp__

42 Cross-term interactions

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

44 Staggering effect

45 Staggering effect Carbon: +1 Lone electron -1/2

46 Polarization

47 Polarization Approximation Electrostatic field does not include contributions from atom i

48 Polarization New model H H O

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

50 Solvent dielectric models Effetive dielectric constant

51 Hydrogen bonds Hydrogen bond is of electrostatic nature. No special term for hydrogen bonds Or potential  is the angle formed by A…H-D

52 Water models SPC, SPC/E, TIP3P TIP4P, BF ST2