Tutorials

1. MolDesign : Computational Molecular Science Workspace

MolDesign is the entry point for all CSE-Online users in the Computational Molecular Science.  For new users, first open MolDesign,  under the 'Help' menu, select  the 'Tour Manager' and then go through the self-guided lessons.   The whole process would take about an hour.

First, please test to see if you can submit jobs to a TeraGrid computer from CSE-Online running on your computer by following step-by-step as shown in this demo movie. Click here to see the movie.

These lessons will allow you to  learn how to use different functionalities available  in MolDesign.   In particular, you will be able to

1. Use MolDesign  to build 3D molecules from atoms and fragments.
2. Use JChemPaint to sketch a 2D  chemical structure then use  SMICAR to convert the 2D to 3D structures.
3. Use Direct Links to the National Cancer Institute (NCI) and National Center for Biotechnology Information Structure Databases.  to search for chemical structures from these databases.
4. Use Gaussian Input Builder to construct input file for  the Gaussian quantum chemistry program.
5. Use GSub to submit/monitor jobs on the TeraGrid computers at the National Center for Supercomputing Applications (NCSA).
6. Use Global File Explorer to manage files on the local desktop and remote servers.  
7. Use Jpeek:  to view a save image.
8. Use Jpad: to view the input and output text files.  
9. Use Pandora to plot the results on a 2D graph.  
10. Use User Feedback to send  feedback to the developing team or image of the current application to a friend.

Future applications to be integrated into MolDesign

Currently these applications are standalone tools.  In the near future from MolDesign you will be able to

1. Use Resource Broker to submit/monitor jobs on any remote servers which the user have login accounts.
2. Use JEKS Spreadsheet to manage results in speadsheet format.
3. Use GAMESS-US Input Builder to prepare input file the GAMESS-US program.
4. Use Quantum Chemistry Knowledge Management System to manage results from quantum chemistry calculations.
5. Use Thermo: to calculate thermodynamic properties of molecular species.
6. Use TheRate: to calculate  rate constants of elementary reactions.
7. Use features in BioViewer: for viewing and analyzing bio-systems.
8. Use Sander-GUI to prepare input files the Sander program (the MD simulation module of the AMBER package).
9. Query and retrieve biological structures from the Protein Data Bank.
10. Use features in Crystal Viewer for viewing and analyzing crystal structures.
11. Use VASP GUI to prepare input files for the VASP periodic DFT program.

Other standalone tools

1. SSH Terminal: SSH Terminal emulator.
2. CSEO messenger: Communication tool for text chat.
3. Jmol: An open-source 3D structure viewer.

2. Computational Chemical Kinetics Workspace

The application framework for the computational chemical kinetics is currently under development.  Below are standalone applications.   

1. Mechanism Editor: A graphic user interface for viewing/editing/analyzing complex mechanisms.
2. PREMIX-GUI: A graphic user interface for creating input for the PREMIX program (part of the CHEMKIN II package).
3. SENKIN-GUI: A graphic user interface for creating input for the SENKIN program (part of the CHEMKIN II package).
4. Mechanism Database: Database for Mechanisms of combustion of hydrocarbons.
5. Flame Database: Database for experimental and calculated premixed flames.

3. Computational Life-Science Workspace

The application framework for the computational life-science is currently underdevelopment.  

1. SWISS Homology: A graphic user interface for the SWISS homology model.

4. Desktop Environment

Click CSE-Online Desktop to learn how to customize the workspace.