1 / 11

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

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

jpetit
Download Presentation

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

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

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

  2. The Project • 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 (though training would be a pain)‏

  3. 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 • Atoms and Atom Collections • Atoms and/or groups governed by rules through their identities

  4. 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 • Also supports via generic apply() method other interactions • Can be generated from arbitrary information • Will be made more generic by having types in themselves be data structures rather than hard-coded enumerations

  5. Molecular Mechanics • Self-Consistent Field Method (SCF)‏ • Iterate over various orientations and shapes, checking for lower energies. • Maximize energy or minimize energy • Genetic Algorithms (more easily made parallel in the future)‏ • Display via dynamically updating 'Rule' view • AtomsViewerRule utilizes a 'view' of an Atom Collection to allow the GUI module to display the simulated system at any point in the simulation

  6. A quick concept, the 'View' • Atom Collections hold static components – what about updating dynamically? • Lone pointers lead to self-confusion, regardless of their classification (smart or other)‏ • Can hold any address, even the smart ones • Have a class that manages atoms by collection • Address them by handle • Asynchronous viewing becomes that much easier. • I mean Asynch in the sense of stepwise – I've yet to go parallel <_<.

  7. Current Images: Yes, I realize that they're crap <_<

  8. What My Molecular Mechanics Section does so far: • Effectively nothing. • It has the rules done • It has the identities done • It has the atom collections done • I/O is essentially done, only trivial matters remain • Energy minimization via genetic algorithms finished but untested (thus – it isn't finished)‏

  9. Ab-initio Methods • Due to my current concentration on MM, I've put very little attention to the ab-initio methods. I'm still reading up on the methods as well as implementations of said methods... But I just haven't had the time to go ahead and do anything. Sorry – but it's the truth! • Ignore the text the previous version had in this area.

  10. 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. • Yeah – ditto on the previous slide's irreverent reference of this area.

  11. Ignore what was here on this slide before >_< Unfortunately, something called 'College' as well as 'I THOUGHT SENIOR YEAR WAS SUPPOSED TO BE EASY???' threw me off on those estimates... Conclusions

More Related