2010 AMS-536 Spring

Instructor	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 3:50PM - 5:10PM
Office Hours	Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics
Teaching Assistant	Sudipto Mukherjee, Room 3-129, 2-8519, 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

Schedule

Note: Each participant please update the Wiki as required with the title of your talk.

Date	Participant	Talk
2010.01.25	First Day of Class Group Study	Organizational Meeting / Mathlab accounts
2010.01.27	Group Study	Visualization software #1, Misc unix skills VMD, MOE, Chimera, vi, general unix cmds, shell scripting
2010.02.01	Group Study	Visualization software #2, Misc unix skills VMD, MOE, Chimera, vi, general unix cmds, shell scripting
2010.02.03	Group Study	Visualization software #3, Misc unix skills VMD, MOE, Chimera, vi, general unix cmds, shell scripting
2010.02.08	Group Study	Tutorials: Group 1=DOCK, Group 2=AMBER
2010.02.10	Group Study	Tutorials: Group 1=DOCK, Group 2=AMBER
2010.02.15	Group Study	Tutorials: Group 1=DOCK, Group 2=AMBER
2010.02.17	Group Study	Tutorials: Group 1=DOCK, Group 2=AMBER
2010.02.22	Group Study	Tutorials: Group 1=AMBER, Group 2=DOCK seawulf accounts / project discussion
2010.02.24	Group Study	Tutorials: Group 1=AMBER, Group 2=DOCK seawulf accounts / project discussion
2010.03.01	Group Study	Tutorials: Group 1=AMBER, Group 2=DOCK seawulf accounts / project discussion
2010.03.03	Group Study	Tutorials: Group 1=AMBER, Group 2=DOCK seawulf accounts / project discussion
2010.03.08	Group Study	Project Setups / Troubleshooting
2010.03.10	Group Study	Project Setups / Troubleshooting
2010.03.15	Group Study	Project Setups / Troubleshooting
2010.03.17	Group Study	Project Setups / Troubleshooting
2010.03.22	Last, First; Last, First	Talk Title ; Talk Title
2010.03.24	Last, First; Last, First	Talk Title ; Talk Title
2010.03.29	SPRING BREAK	NO CLASS
2010.03.31	SPRING BREAK	NO CLASS
2010.04.05	Last, First; Last, First	Talk Title ; Talk Title
2010.04.07	Last, First; Last, First	Talk Title ; Talk Title
2010.04.12	Preliminary Report Due Last, First; Last, First;	Talk Title ; Talk Title
2010.04.14	Last, First; Last, First	Talk Title ; Talk Title
2010.04.19	Last, First; Last, First	Talk Title ; Talk Title
2010.04.21	Last, First; Last, First	Talk Title ; Talk Title
2010.04.26	Last, First; Last, First	Talk Title ; Talk Title
2010.04.28	Last, First; Last, First	Talk Title ; Talk Title
2010.05.03	Last, First; Last, First	Talk Title ; Talk Title
2010.05.05	Last Day of Class Group Study	Project Discussion
2010.05.??	Final written report due by 10AM, May ??, 2010. Late papers will not be accepted. See above for sample reports and detailed guidelines.	Give hard copy to Sudipto Mukherjee (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com