Molecular Simulation PowerPoint Presentation

Molecular Simulation PowerPoint Presentation

2017-01-19 43K 43 0 0

Description

Molecular Simluation. Introduction:. Prerequisition: . A powerful computer, fast graphics card,. An efficient way to solve Schroedingers wave equation for many atoms,. A reliable structure or structural model. ID: 511426

Embed code:

Download this presentation



DownloadNote - The PPT/PDF document "Molecular Simulation" is the property of its rightful owner. Permission is granted to download and print the materials on this web site for personal, non-commercial use only, and to display it on your personal computer provided you do not modify the materials and that you retain all copyright notices contained in the materials. By downloading content from our website, you accept the terms of this agreement.

Presentations text content in Molecular Simulation

Slide1

Molecular Simulation

Slide2

Molecular Simluation

Introduction:

Prerequisition:

A powerful computer, fast graphics card,

An efficient way to solve Schroedingers wave equation for many atoms,

A reliable structure or structural model

Slide3

Molecular Simluation

Structures or reliable model structures:

X-ray crystallography

NMR spectroscopy

Homology modelling

Slide4

Molecular Simulation

Where do we get the structures from?

Databases

Brookhaven protein data base

Or homology models

Slide5

Molecular Simulation

Homology modelling:

Slide6

Slide7

Slide8

Slide9

Slide10

Slide11

Slide12

Slide13

Slide14

Slide15

Slide16

Slide17

Slide18

Slide19

Slide20

Slide21

Slide22

Slide23

Slide24

Slide25

Slide26

Slide27

Slide28

Slide29

Slide30

Molecular Simulation

Molecular Mechanics:

The Potential energy surface (PES):

Born-Oppenheimer approx. allows us to separate electronic and nuclear motion

when nuclei move, the electrons re-adjust quickly

energy of molecule is a function of the positions of the nuclei

potential energy surface describes energy of a molecule in terms of its structure

Slide31

Molecular Simulation

Slide32

Molecular Simulation

Structure

determined from the potential energy surface

minimum corresponds to an equilibrium structure

first order saddle point corresponds to a transition state for a reaction

a reaction path is the steepest descent path connecting a transition state to minima

Dynamics

molecules move on the potential energy surface

dynamics can be treated classically or quantum mechanically

small amplitude motions - normal modes of vibration

large amplitude motions - trajectories, wave packets, reactions

statistical mechanics to connect microscopic to macroscopic

Slide33

Molecular Simulation

Bond stretching

Valence angle bending

Torsions

Van der Waals Interactions

Electrostatic Interactions

Cross terms

Slide34

Molecular Simulation

Bond Stretching and valence angle bending

Slide35

Molecular Simulations

Torsions

Slide36

Molecular Simulation

Interaction of 2 point charges

Slide37

Molecular Simulation

Van der Waals Interactions

Slide38

Molecular Simulation

Force Field Energies

Geometry Optimisation

Thermodynamics

Slide39

Molecular Simulation

Modern Force Fields

CHARMM Biomolecules

CHARMm Bio and org. molecules

CFF/CVFF org. and bio molecules

GROMOS Biomolecules

MM2 organics

MM3 org. and bio molecules

OPLS all-atom and united atom version

SYBYL/TRIPOS org. and bio molecules


About DocSlides
DocSlides allows users to easily upload and share presentations, PDF documents, and images.Share your documents with the world , watch,share and upload any time you want. How can you benefit from using DocSlides? DocSlides consists documents from individuals and organizations on topics ranging from technology and business to travel, health, and education. Find and search for what interests you, and learn from people and more. You can also download DocSlides to read or reference later.