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Exploring C-Chem with numeric MM and Ab-Initio methods

Masood Malekghassemi. Exploring C-Chem with numeric MM and Ab-Initio methods. What the heck is up with this janx?. Comptuational Chemistry Methods Step 1: Molecular Mechanics Step 2: Ab-initio quantum chemical methods

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Exploring C-Chem with numeric MM and Ab-Initio methods

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  1. Masood Malekghassemi Exploring C-Chem with numeric MM and Ab-Initio methods

  2. What the heck is up with this janx? • Comptuational Chemistry Methods • Step 1: Molecular Mechanics • Step 2: Ab-initio quantum chemical methods • Analysis and translation of Ab-initio quantum chemical methods to molecular mechanics rules • Step 3: Artificial Intelligence, neural network sounds proper for the application

  3. Molecular Mechanics

  4. Molecular Mechanics • Identities • The different kinds of atoms and/or groups – may be particular atoms in specific functional groups • Rules • Governs the quantization of energy of particular shapes and orientations of the molecule's constituents • Constituents • Atoms and/or groups governed by rules through their identities

  5. The Rules • The rules are the main difference between this program and other molecular mechanics programs • Provides a generic interface to govern a system through energetic interactions • See MM class hierarchy on slide 3 • Can be generated from arbitrary information • Will be made more generic by having types in themselves be data structures rather than hard-coded enumerations

  6. Molecular Mechanics • Self-Consistent Field Method (SCF) • Iterate over various orientations and shapes, checking for lower energies. • Maximize energy or minimize energy • Hill-climbing • Portray via file and/or a basic GUI (perhaps using Irrlicht or Ogre3D, rather than homebrew, to simplify process)

  7. What My Molecular Mechanics Section does so far: • Effectively nothing. • It has the rules done • It has the identities done • It has the constituents done • It does not have fully working I/O • I've been debating with myself over the trivial matter of file format for too long • It does not have the iterative SCF method implemented yet

  8. Ab-initio Methods • Due to my current concentration on MM, I've put very little attention to the ab-initio methods. However, I've already gotten started somewhat on its coding by making a generalized integrator that finds the average of a function via point generator (thus allowing easy implementation of multiple Monte Carlo methods using the same interface) and then multiplies it by the area of its domain • Talk to me in about a month for actual planning and diagrams

  9. Artificial Intelligence • This is the lofty goal of the project. If I only finished up to the end of my molecular mechanics part or ab-initio part I'd be happy. However... This'd be amazing awesome to get started on and done with. • Talk to me in about two or three months for actual planning and diagrams of the AI idea

  10. The gist of it: Talk to me in five to six months, and I swear to you, I'll have the thing working :-P Conclusions

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