分子模拟与设计基本理论 PPT.pdf

分子模拟与设计 基本理论 1 Outlines Force Fields Solvation Models Molecular Dynamics Advanced Topics on MD Molecular Design 2 Force Field 3 Hierarchy of theoretical models: a look at space time scales computational approaches to molecular science focus on systems from the quantum world to the mesoscale 4 Principle of Molecular Dynamics Schrödinger equation Born-Oppenheimer approximation Nucleic motion described classically Empirical force field 5 Coarse-grained model Different time-spatial scale for different phenomenon 6 Molecular Mechanics – Apply classical physics to molecules – No electrons, orbitals, wavefunctions, etc. – Bonds are springs that obey Hooke’s Law – Bond angles and dihedral angles are also mathematically treated as springs – Charge interactions: Coulomb’s Law – Other interactions (van der Waals, Hydrogen bonding, etc.) have simple mathematical constructs 7 7 Molecular Mechanics 8 Bonded Atoms There are three types of interaction between