江苏江阴农好村商业银行股份有限公司j47.pptVIP

Molecular Mechanics Part 2 Potential Energy Surfaces Input File Types Successes, Limitations Caveats Glossary of Terms Energy Minimization Local minimum vs global minimum Many local minima; only ONE global minimum Methods: Newton-Raphson (block diagonal), steepest descent, conjugate gradient, others. Potential Energy Surface PES and Energy Minimization First, some caveats: extrema (stationary points) are located by most methods; this includes maxima, minima, and saddle points. among the minima, local minima are found, not necessarily the global minimum. with shallow minima (flat PES), a lot of cpu time can be spent seeking the lowest energy structure. Approaches to Global Minimum Dihedral driving (manual or automated; a 3n) Randomization-minimization (Monte Carlo) Molecular dynamics Trial error (poor) All methods are tedious, but some attempt at searching for the minimum is absolutely necessary if the result is to be meaningful! Input File Structure Input is usually done graphically (by sketching or building structures atom-by-atom or by assembling component parts). This graphical model is converted to a mathematical model by the software. Each software package has its own file type, but most have some common features. The .pdb file is most common denominator. PDB (protein data bank) file of propane (C3H8) HETATM 1 C 1 -1.129 1.281 -0.000 HETATM 2 C 2 -2.558 1.772 -0.000 HETATM 3 C 3 -3.519 0.606 -0.000 HETATM 4 H 4 -0.596 1.637 0.890 HETATM 5 H 5 -0.596 1.637 -0.890 HETATM 6 H 6 -2.733 2.392 0.890 HETATM 7 H 7 -2.733 2.392 -0.890 HETATM 8 H 8 -4.558 0.952 0.000 HETATM 9 H 9 -3.359 -0.017 -0.890 HETATM 10 H 10 -3.359 -0.017 0.890 HETATM 11 H 11 -1.110 0.183 -0.000 continued... (not all columns utilized/recognized by all software) …bottom of .PDB file CONECT 1 2