Introduction to Molecular Mechanics - Mahidol University

More documents

Recommendations

Info

Force Field Molecular Modeling Molecular Mechanics needs to know force constants and equilibrium geometry of all springs. This set of parameters is called “Force Field parameters”. ATOM TYPE C(sp3): C1 C(carbonyl): C2 O(C=O): O1 O(acid): O2 H: H1, H2, H3 H(acid): H4 k str : C(sp3)-C(carbonyl), C(sp3)-H, …. k bnd : H-C(sp3)-C(carbonyl), …… k tor : H-C(sp3)-C(carbonyl)-O(acid), … R 0 : C(sp3)-C(carbonyl), ….. And all equilibrium angles, torsion plus van der Waals parameters and partial charges
Force Field Molecular Modeling Examples of MM2 carbon atom type
Page 1 and 2: Teerakiat Kerdcharoen, Mahidol Univ
Page 3 and 4: Molecular Model • Quantum Mechani
Page 5 and 6: Electronic Structure Nanoscience Ma
Page 7 and 8: Energy Nanoscience Mahidol Univ Exa
Page 9 and 10: Molecular Mechanics Nanoscience Mah
Page 11 and 12: Molecular Mechanics Molecular Model
Page 13 and 14: Energy expression Molecular Modelin
Page 15 and 16: Cross term Molecular Modeling Cross
Page 17 and 18: Non-bond interaction Molecular Mode
Page 19 and 20: Non-bond interaction Molecular Mode
Page 21 and 22: Electrostatic This slide is reprodu
Page 23: Sum of energy Molecular Modeling Su
Page 27 and 28: Force Field Molecular Modeling http
Page 29 and 30: Force field’s availability
Page 31 and 32: Common Approximation • Ignore hyd
Page 33 and 34: Energy Minimization Initial structu
Page 35: Simulated Annealing Temperature Hea

Introduction to Molecular Mechanics - Mahidol University

Create successful ePaper yourself

Delete template?

Save as template?