Try  HackMD Logo HackMD

Structure models

Given the structure of a molecule, this Matlab code simulates the vibrational spectrum based upon on the coupled oscillator model. Currently, COSMOSS supports the following structural construction models:

  • Two coupled-oscillators
  • Amide-I modes of peptide from PDB file
  • 2D-Grid built from formatted quantum simulation outputs, such as Gaussian 09.
  • Amide-I modes of an ideal beta-sheet
  • Combination of any two models above

Construct your own model

COSMOSS is designed to be expandable! You can generate the molecule that you are interested in and use the COSMOSS core to calculate its spectrum. Check the definition of the StructureData Class for more information.

More tutorials is coming soon…

tags: tutorials COSMOSS
Last changed by 
 
Jia-Jung Ho
0
509

Read more

How to edit COSMOSS GUIs

The Graphic User Interfaces (GUIs) of COSMOSS were written with the appdesigner of Matlb. I used to use GUIDE wordle for the GUIs but found the appdesigner is much scalable. Editing Main GUI To edit the GUIs, you need to call the appdesigner command with the '.mlapp' files. For example, to edit the main GUI, I can type the following in the Matlab working space[^PS]: > appdesigner COSMOSS You should see the appdesigner interface shows up as following: The above figure shows the design view, which allows you to edit the graphical elements. The other tab on the top right named 'Code View' will give you access to the source code for further editing:

Jan 8, 2024
TODO list

Here is a list of tasks to improve COSMOSS in various aspects: Last edited: [name=JJHo] [time= Sep 21, 2020] [color=#ff4233] Documentations related Coding tutorials/documentations: [x] Need to update the isotope labeling tutorial [x] Write about the analysis tools

Jul 12, 2021
What is COSMOSS?

:::info COSMOSS is a Coupled OScillator MOdel Spectral Simulator ::: Initially COSMOSS was created for my PhD research projects. Using the coupled-oscillators framework, I simulated and extracted information from experimental spectrum[^GoogleScholar], mostly on 2D IR and 2D SFG. As the COSMOSS project moving forward, I couldn't help but wonder if I can make it more general (as its name implied), i.e. works for different molecules, with a user-friendly GUI, support other spectral types, and most important of all, it is open source! So here is it, hope you enjoy it. What can COSMOSS do? COSMOSS can help you generate model structures and simulated their vibrational spectrum, currently includes:

Jun 20, 2021
Coding structure

COSMOSS is a Matlab based program. The Graphic User Interfaces(GUI) end can be break down in to three parts: Structure model generation (model_GUIs) Spectral simulations (main_GUI) Spectral analysis (tool_GUIs) graph LR subgraph Summary of GUIs A1(Two-coupled oscillators) -->B

Jun 20, 2021
Read more from Jia-Jung Ho
Published on HackMD