2013 AMS-536 Spring

Instructor	Dr. William J. Allen [631-632-8519, william.allen@stonybrook.edu] Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com]
Course No.	AMS-536 / CHE-536
Location/Time	Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:20PM - 3:40PM
Office Hours	Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
Teaching Assistant	Yuchen Zhou, Math Tower, Room 3-129, Dept. of Applied Math & Statistics

Project Information

Project Approval Sheet

• project.student.info.doc

Oral Presentation Guidlines: These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be 30 minutes long. The purpose of your talks is for you to clearly and concisely present your overall progress to date including appropriate background material and interpretation of your results. Talks should be arranged in the following order:

• Introduction/Background (include biological relevance)
• Specifics of Your System
• Computational Details (theory)
• Computational Details (system setup)
• Results and Discussion (include a critical interpretation of your results)
• Conclusions
• Future
• Acknowledgments

Final Report Guidelines and Example Final Papers

• project.guidelines.pdf
• project.example.dGhyd.pdf
• project.example.MMPS.pdf

Tutorials, Software Links, and Other Relevant Class Information

• Rizzo_Lab_Information_and_Tutorials
• Cheat Sheet: Unix, Vi, C_Shell_Scripting

Schedule

• Each participant please update the Wiki as required with the title of your talk.
• Please note that a doctors excuse will be required if you miss your scheduled oral presentation date because of illness.

Date	Participant	Talk
2013.01.28	First Day of Class and Organizational Meeting Group Study	Mathlab account setup Discuss research paper and presentations handouts for unix / vim / csh tutorials
2013.01.30	Group Study	Confirm Mathlab accounts work Go over unix / vim / csh tutorials Seawulf account setup
2013.02.04	Group Study	Continue unix / vim / csh tutorials Logging into Seawulf
2013.02.06	Group Study	Finish unix / vim / csh tutorials Csh scripting exercises Transfering files to Seawulf
2013.02.11	Group Study	Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix
2013.02.13	Group Study	Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix
2013.02.18	Group Study	Tutorials: DOCK individual project discussion Allen, W.
2013.02.20	Group Study	Tutorials: DOCK individual project discussion
2013.02.25	Group Study	Tutorials: DOCK individual project discussion
2013.02.27	Group Study	Tutorials: DOCK individual project discussion
2013.03.04	Group Study	Tutorials: DOCK wiki editing
2013.03.06	Group Study	Tutorials: AMBER individual project discussion Jiang L.
2013.03.11	Group Study	Tutorials: AMBER individual project discussion
2013.03.13	Group Study	Tutorials: AMBER individual project discussion
2013.03.18	Spring Recess	Spring Recess
2013.03.20	Spring Recess	Spring Recess
2013.03.25	Group Study	Tutorials: AMBER individual project discussion
2013.03.27	Group Study	Tutorials: AMBER wiki editing
2013.04.01	Deadline for project proposal discussion Group Study	Project Setups / Troubleshooting
2013.04.03	Group Study	Project Setups / Troubleshooting
2013.04.08	TBD	Project Proposal
2013.04.10	TBD	Project Proposal
2013.04.15	TBD	Project Proposal
2013.04.17	Preliminary Report Due TBD	Project Proposal
2013.04.22	TBD	Project Proposal
2013.04.24	TBD	Progress Report
2013.04.29	TBD	Progress Report
2013.05.01	TBD	Progress Report
2013.05.06	TBD	Progress Report
2013.05.08	Last Day of Class TBD	Progress Report
2013.05.15	Final written report due by 5PM today. Late papers will not be accepted. See above for sample reports and detailed guidelines.	Give hard copy to Yuchen Zhou (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com